[English] 日本語
Yorodumi
- PDB-6u39: 2.4 Angstrom crystal structure of the D129G Ca-CaM:CaV1.2 IQ doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u39
Title2.4 Angstrom crystal structure of the D129G Ca-CaM:CaV1.2 IQ domain complex
Components
  • Calmodulin-1
  • Voltage-dependent L-type calcium channel subunit alpha-1C
KeywordsCALCIUM-BINDING PROTEIN/MEMBRANE PROTEIN / MEMBRANE PROTEIN / CALCIUM-BINDING PROTEIN-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


: / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during AV node cell action potential / positive regulation of adenylate cyclase activity / cardiac conduction ...: / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during AV node cell action potential / positive regulation of adenylate cyclase activity / cardiac conduction / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell action potential / high voltage-gated calcium channel activity / camera-type eye development / NCAM1 interactions / embryonic forelimb morphogenesis / CaM pathway / Cam-PDE 1 activation / calcium ion transport into cytosol / Sodium/Calcium exchangers / cell communication by electrical coupling involved in cardiac conduction / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / voltage-gated calcium channel complex / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / regulation of heart rate by cardiac conduction / alpha-actinin binding / RHO GTPases activate PAKs / calcium ion import across plasma membrane / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / voltage-gated calcium channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / VEGFR2 mediated cell proliferation / Regulation of insulin secretion / Translocation of SLC2A4 (GLUT4) to the plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated ...Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Voltage-dependent channel domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Voltage-dependent L-type calcium channel subunit alpha-1C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, K. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J. Physiol. (Lond.) / Year: 2020
Title: Arrhythmia mutations in calmodulin can disrupt cooperativity of Ca2+binding and cause misfolding.
Authors: Wang, K. / Brohus, M. / Holt, C. / Overgaard, M.T. / Wimmer, R. / Van Petegem, F.
History
DepositionAug 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin-1
B: Voltage-dependent L-type calcium channel subunit alpha-1C
C: Calmodulin-1
D: Voltage-dependent L-type calcium channel subunit alpha-1C
E: Calmodulin-1
F: Voltage-dependent L-type calcium channel subunit alpha-1C
G: Calmodulin-1
H: Voltage-dependent L-type calcium channel subunit alpha-1C
I: Calmodulin-1
J: Voltage-dependent L-type calcium channel subunit alpha-1C
K: Calmodulin-1
L: Voltage-dependent L-type calcium channel subunit alpha-1C
M: Calmodulin-1
N: Voltage-dependent L-type calcium channel subunit alpha-1C
O: Calmodulin-1
P: Voltage-dependent L-type calcium channel subunit alpha-1C
Q: Calmodulin-1
R: Voltage-dependent L-type calcium channel subunit alpha-1C
S: Calmodulin-1
T: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,98549
Polymers209,82320
Non-polymers1,16229
Water36020
1
A: Calmodulin-1
B: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-51 kcal/mol
Surface area9530 Å2
MethodPISA
2
C: Calmodulin-1
D: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-65 kcal/mol
Surface area10080 Å2
MethodPISA
3
E: Calmodulin-1
F: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-59 kcal/mol
Surface area10080 Å2
MethodPISA
4
G: Calmodulin-1
H: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-50 kcal/mol
Surface area10020 Å2
MethodPISA
5
I: Calmodulin-1
J: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0624
Polymers20,9822
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-51 kcal/mol
Surface area9610 Å2
MethodPISA
6
K: Calmodulin-1
L: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-61 kcal/mol
Surface area10220 Å2
MethodPISA
7
M: Calmodulin-1
N: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-48 kcal/mol
Surface area9610 Å2
MethodPISA
8
O: Calmodulin-1
P: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-49 kcal/mol
Surface area9680 Å2
MethodPISA
9
Q: Calmodulin-1
R: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-63 kcal/mol
Surface area9800 Å2
MethodPISA
10
S: Calmodulin-1
T: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1035
Polymers20,9822
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-63 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.795, 161.656, 96.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Calmodulin-1 /


Mass: 16663.312 Da / Num. of mol.: 10 / Mutation: D129G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein/peptide
Voltage-dependent L-type calcium channel subunit alpha-1C / Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Voltage-gated calcium ...Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Voltage-gated calcium channel subunit alpha Cav1.2


Mass: 4318.968 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CACNA1C, CACH2, CACN2, CACNL1A1, CCHL1A1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13936
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→49.041 Å / Num. obs: 159034 / % possible obs: 97.5 % / Redundancy: 2.93 % / Biso Wilson estimate: 68.18 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.06
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
2.3-2.44257110.7991
2.44-2.61242850.9291
6.84-49.04160410.9981

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G43
Resolution: 2.4→49.041 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 31.89
RfactorNum. reflection% reflection
Rfree0.2827 6993 4.99 %
Rwork0.2318 --
obs0.2344 140090 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.25 Å2 / Biso mean: 85.4384 Å2 / Biso min: 40.19 Å2
Refinement stepCycle: final / Resolution: 2.4→49.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11328 0 29 20 11377
Biso mean--82.34 67.99 -
Num. residues----1596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.42730.36142370.3135446898
2.4273-2.45580.37572330.2965441198
2.4558-2.48580.38962300.3021445797
2.4858-2.51720.32972380.2966445599
2.5172-2.55040.32142360.2839449999
2.5504-2.58530.33942380.2778450899
2.5853-2.62220.32332290.2816442798
2.6222-2.66140.36672370.2869449298
2.6614-2.70290.36782320.2912445898
2.7029-2.74730.33572340.2816445899
2.7473-2.79460.36272370.3004449798
2.7946-2.84540.40182390.2979447198
2.8454-2.90020.36342370.3035443698
2.9002-2.95940.3452310.2974443698
2.9594-3.02370.34442290.3059442097
3.0237-3.0940.35912360.3022447998
3.094-3.17140.35282390.3056450198
3.1714-3.25710.28862360.265446399
3.2571-3.35290.31472330.2467446598
3.3529-3.46110.35362290.2571437396
3.4611-3.58480.3352350.2552444098
3.5848-3.72830.30792160.2426420692
3.7283-3.89790.2712350.2164430095
3.8979-4.10330.25052250.2098437596
4.1033-4.36020.2512330.1932445798
4.3602-4.69660.23372330.1908446098
4.6966-5.16880.26812340.1902443097
5.1688-5.91570.31172320.2464438997
5.9157-7.44890.2672320.2419444298
7.4489-49.040.20142280.1811442497
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.2054-2.65322.23393.7614-0.6836.21590.56030.2866-1.7957-0.2333-0.05370.29051.1840.0643-0.54180.7446-0.0768-0.01840.7029-0.24841.123114.3488-2.193339.4294
27.0228-4.1757-2.86543.21972.2111.9635-0.13350.1044-0.55870.0923-0.05030.55440.0676-0.0090.14160.56910.04940.05070.605-0.06750.697727.35194.225447.7085
37.41711.8020.1222.17982.51984.27360.88630.28371.08271.2379-0.15651.0371-0.11-0.3314-0.7720.84750.10390.19850.588-0.08831.000318.286310.69744.3165
45.77813.7596-1.58154.57911.96658.37610.5807-0.69680.42821.0548-0.62470.4536-0.2924-0.01630.05270.6972-0.02130.04550.5246-0.06240.651648.519411.984759.0472
58.3697-5.852-0.80866.06671.46241.4888-0.2656-0.55010.53890.38860.3788-0.52530.15890.3105-0.12780.46520.01620.06380.4364-0.02330.596434.09896.651450.8404
64.32550.76774.25786.24751.54064.3686-0.03730.65641.5146-0.1773-0.4448-0.2649-0.21550.70760.46230.54850.01420.02930.5804-0.0340.717246.92078.065746.6193
76.01510.0554-0.80799.30241.35974.41310.2705-0.04460.0540.3408-0.1268-0.6659-0.39370.1491-0.09670.54160.03320.11470.49840.07190.596617.601134.883360.5373
87.0887-4.95510.69364.9849-1.07230.8522-0.1702-0.6432-0.23750.2560.41270.147-0.1114-0.1747-0.24620.6917-0.11610.02460.57620.12130.761432.961142.85555.4943
95.39265.6827-5.72415.8894-5.86415.8201-0.43281.0255-0.058-0.18410.078-0.6528-0.1749-0.61670.40330.8987-0.0260.140.74030.05040.992324.390442.411949.1169
106.5117-0.32980.23269.53131.2626.3668-0.05980.3603-0.0657-0.20170.1159-0.2691-0.01210.1593-0.01730.4366-0.0660.02460.4969-0.00850.433756.850956.43667.0603
118.7-0.98534.58210.0752-1.63642.98140.13820.57370.0333-0.1933-0.396-0.01770.06930.13130.23180.61440.0763-0.02670.7382-0.10210.530543.289359.555818.3269
124.2694.6013-4.37787.743-6.3555.7591-0.28670.0431-2.03070.1559-0.782-0.73480.1098-0.59460.76180.6748-0.0558-0.04730.7823-0.0510.641450.70252.046421.3101
135.15771.67250.23365.4536-4.28277.73470.2970.1286-0.2442-0.42260.0732-0.01080.48990.025-0.41280.6310.1454-0.00190.5549-0.15280.548945.5363-10.782923.1961
146.4607-1.265-4.95950.83970.10415.15810.1858-0.6324-0.5418-0.0341-0.0983-0.1484-0.06830.3554-0.06150.6860.0828-0.18520.8836-0.1620.747933.7009-3.311712.5215
157.2275-4.07381.6767.7689-4.35132.4352-0.29830.61380.4824-0.25940.2275-0.1285-0.3375-0.68960.25081.0160.0101-0.03241.0463-0.08020.627244.6965-0.186514.6041
168.15650.87420.13524.1037-2.89178.25010.3155-0.1892-0.5181-0.4428-0.4273-0.34880.30320.53120.10390.57510.0392-0.11040.5166-0.0130.771216.07235.563-2.4206
177.82090.8155-4.0209-0.1041-0.22281.8026-0.25640.5241-0.5371-0.2457-0.0774-0.03550.128-0.49890.24380.6896-0.01-0.24160.9825-0.070.935428.9478-0.19158.0999
185.7023-5.28845.59014.8052-4.97445.2831-0.0815-2.01810.35860.61840.1965-0.92890.101-0.93180.13240.84860.1096-0.08550.869-0.08210.704616.29075.235911.0175
195.5938-2.0847-1.32855.27764.51345.65780.37960.1203-0.0439-0.89270.009-1.0197-0.6875-0.0768-0.31140.935-0.0845-0.07640.561-0.0620.7722.506348.3988-5.3765
209.23572.05541.10761.44260.21260.49620.1280.78410.4882-0.11770.03680.2862-0.03490.1413-0.23520.74980.0109-0.07360.6466-0.10270.762235.212535.5535-7.6217
218.8879-8.25936.85989.8086-6.80115.28480.6366-1.2048-0.411-0.65750.3907-0.46341.1606-1.1777-0.92650.9433-0.2154-0.0680.8407-0.18540.905623.67534.3345-1.978
226.0661.3488-0.66766.9077-0.9244.73910.5237-0.52960.45211.15870.0110.1281-0.1494-0.4771-0.54250.6437-0.0738-0.02370.65280.10320.640654.457853.137649.7493
238.1068-4.95423.41795.4505-1.47130.89220.08260.09130.7310.3803-0.2498-0.56590.01410.16180.21640.6268-0.11410.08180.64820.09110.651139.131145.610454.4461
248.38112.94793.89346.70160.94992.78190.46810.8194-0.76240.27460.52060.49740.8496-0.0932-0.96180.8428-0.1473-0.05620.6960.13820.705249.029139.789550.195
257.4925-4.92470.3396.4216-0.33227.82150.58490.69610.4791-0.8633-1.046-0.2237-0.0131.37830.4920.64290.12820.0360.69670.11320.705725.176766.624132.6314
264.5743-0.60522.20181.38410.93521.7776-0.0862-0.01150.7315-0.2855-0.41610.1636-0.4078-0.32340.52440.57060.07920.0110.91250.02670.605739.937760.144424.5212
273.0198-1.1096-2.0079.37235.11293.97190.2921.094-1.0111-0.3365-0.32510.47061.0343-0.29280.070.77530.1474-0.12050.8221-0.0040.568325.389257.379321.5908
284.0798-3.8279-5.27494.18124.94276.59130.7474-1.11020.496-0.23440.6661-0.6843-0.52321.1856-1.27581.0884-0.14110.02431.0519-0.14830.905949.597529.3816-2.0946
293.5067-2.16351.67588.3788-5.71779.21881.14370.7395-0.5315-1.5533-0.75910.75080.96210.3178-0.35210.910.043-0.09530.8041-0.06520.808550.331317.0175-9.6241
307.05852.57730.25850.68140.72350.7959-0.38510.717-0.898-0.47770.3974-0.1290.05630.1086-0.03810.6434-0.05060.00760.7289-0.08460.904538.869930.2886-8.4845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 501 through 502) or (resid 6 through 76))A0
2X-RAY DIFFRACTION2chain 'A' and ((resid 82 through 147) or (resid 503))A0
3X-RAY DIFFRACTION3chain 'B' and (resid 1612 through 1634)B1612 - 1634
4X-RAY DIFFRACTION4chain 'C' and ((resid 5 through 75) or (resid 501 through 502))C0
5X-RAY DIFFRACTION5chain 'C' and ((resid 82 through 148) or (resid 503))C0
6X-RAY DIFFRACTION6chain 'D' and (resid 1609 through 1634)D1609 - 1634
7X-RAY DIFFRACTION7chain 'E' and ((resid 501 through 502) or (resid 3 through 77))E0
8X-RAY DIFFRACTION8chain 'E' and ((resid 81 through 147) or (resid 503))E0
9X-RAY DIFFRACTION9chain 'F' and (resid 1614 through 1636)F1614 - 1636
10X-RAY DIFFRACTION10chain 'K' and ((resid 501 through 502) or (resid 4 through 77))K0
11X-RAY DIFFRACTION11chain 'K' and ((resid 81 through 147) or (resid 503))K0
12X-RAY DIFFRACTION12chain 'L' and (resid 1614 through 1637)L1614 - 1637
13X-RAY DIFFRACTION13chain 'S' and ((resid 501 through 502) or (resid 4 through 76))S0
14X-RAY DIFFRACTION14chain 'S' and ((resid 83 through 147) or (resid 503))S0
15X-RAY DIFFRACTION15chain 'T' and (resid 1613 through 1632)T1613 - 1632
16X-RAY DIFFRACTION16chain 'Q' and ((resid 501 through 502) or (resid 4 through 74))Q0
17X-RAY DIFFRACTION17chain 'Q' and ((resid 82 through 147) or (resid 503))Q0
18X-RAY DIFFRACTION18chain 'R' and (resid 1609 through 1633)R1609 - 1633
19X-RAY DIFFRACTION19chain 'M' and ((resid 501 through 502) or (resid 5 through 75))M0
20X-RAY DIFFRACTION20chain 'M' and ((resid 84 through 147) or (resid 503))M0
21X-RAY DIFFRACTION21chain 'N' and (resid 1612 through 1635)N1612 - 1635
22X-RAY DIFFRACTION22chain 'G' and ((resid 501 through 502) or (resid 4 through 76))G0
23X-RAY DIFFRACTION23chain 'G' and ((resid 84 through 146) or (resid 503))G0
24X-RAY DIFFRACTION24chain 'H' and (resid 1612 through 1635)H1612 - 1635
25X-RAY DIFFRACTION25chain 'I' and ((resid 501 through 502) or (resid 7 through 75))I0
26X-RAY DIFFRACTION26chain 'I' and (resid 82 through 147)I82 - 147
27X-RAY DIFFRACTION27chain 'J' and (resid 1610 through 1635)J1610 - 1635
28X-RAY DIFFRACTION28chain 'P' and (resid 1613 through 1633)P1613 - 1633
29X-RAY DIFFRACTION29chain 'O' and ((resid 501 through 502) or (resid 4 through 74))O0
30X-RAY DIFFRACTION30chain 'O' and ((resid 84 through 147) or (resid 503))O0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more