[English] 日本語
Yorodumi
- PDB-3glf: Crystal Structure of the Ecoli Clamp Loader Bound to Primer-Templ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3glf
TitleCrystal Structure of the Ecoli Clamp Loader Bound to Primer-Template DNA
Components
  • (DNA polymerase III subunit ...DNA polymerase III holoenzyme) x 3
  • DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')
  • DNA (5'-D(*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3')
KeywordsTransferase/DNA / AAA+ ATPase / Clamp Loader / Gamma Complex / Replication / DNA replication / DNA-directed DNA polymerase / Nucleotidyltransferase / Transferase / ATP-binding / Nucleotide-binding / Transferase-DNA COMPLEX
Function / homology
Function and homology information


DNA polymerase III, clamp loader complex / DNA clamp loader activity / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase ...DNA polymerase III, clamp loader complex / DNA clamp loader activity / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit ...Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit / DNA polymerase III delta, N-terminal / DNA polymerase III, delta subunit / DNA polymerase III, tau subunit, domain V / DNA polymerase III subunit tau, DnaB-binding domain IV / DNA polymerase III, tau subunit, domain V superfamily / DNA polymerase III, subunit gamma/tau, helical lid domain / DNA polymerase III subunits tau domain IV DnaB-binding / DNA polymerase III tau subunit V interacting with alpha / DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III / DNA polymerase III, delta subunit / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 - #60 / ClpA/B family / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA polymerase III subunit tau / DNA polymerase III subunit delta / DNA polymerase III subunit delta'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.388 Å
AuthorsSimonetta, K.R. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.
Authors: Simonetta, K.R. / Kazmirski, S.L. / Goedken, E.R. / Cantor, A.J. / Kelch, B.A. / McNally, R. / Seyedin, S.N. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase III subunit delta
B: DNA polymerase III subunit tau
C: DNA polymerase III subunit tau
D: DNA polymerase III subunit tau
E: DNA polymerase III subunit delta'
F: DNA polymerase III subunit delta
G: DNA polymerase III subunit tau
H: DNA polymerase III subunit tau
I: DNA polymerase III subunit tau
J: DNA polymerase III subunit delta'
K: DNA (5'-D(*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3')
L: DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')
M: DNA (5'-D(*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3')
N: DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,03440
Polymers430,40514
Non-polymers3,62826
Water0
1
A: DNA polymerase III subunit delta
B: DNA polymerase III subunit tau
C: DNA polymerase III subunit tau
D: DNA polymerase III subunit tau
E: DNA polymerase III subunit delta'
K: DNA (5'-D(*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3')
L: DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,01720
Polymers215,2037
Non-polymers1,81413
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26190 Å2
ΔGint-142 kcal/mol
Surface area74760 Å2
MethodPISA
2
F: DNA polymerase III subunit delta
G: DNA polymerase III subunit tau
H: DNA polymerase III subunit tau
I: DNA polymerase III subunit tau
J: DNA polymerase III subunit delta'
M: DNA (5'-D(*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3')
N: DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,01720
Polymers215,2037
Non-polymers1,81413
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26840 Å2
ΔGint-140 kcal/mol
Surface area75740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.264, 219.947, 273.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C and (resseq 4:368 or resseq 400:403)
21chain H and (resseq 4:368 or resseq 400:403)
12chain D and (resseq 2:363 or resseq 400:403)
22chain I and (resseq 2:363 or resseq 400:403)
13chain B and (resseq 5:368 or resseq 400:403)
23chain G and (resseq 5:368 or resseq 400:403)
14chain E and (resseq 1:334 or resseq 403)
24chain J and (resseq 1:334 or resseq 403)
15chain A and (resseq 1:333 )
25chain F and (resseq 1:333 )
16chain K or chain L
26chain M or chain N

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111CC4 - 3684 - 368
121CC400 - 403400 - 403
211HH4 - 3684 - 368
221HH400 - 403400 - 403
112DD2 - 3632 - 363
122DD400 - 403400 - 403
212II2 - 3632 - 363
222II400 - 403400 - 403
113BB5 - 3685 - 368
123BB400 - 403400 - 403
213GG5 - 3685 - 368
223GG400 - 403400 - 403
114EE1 - 3341 - 334
124EE403 - 0403 - 0
214JJ1 - 3341 - 334
224JJ403 - 0403 - 0
115AA1 - 3331 - 333
215FF1 - 3331 - 333
116KK2 - 152 - 15
216MM2 - 152 - 15

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
DNA polymerase III subunit ... , 3 types, 10 molecules AFBCDGHIEJ

#1: Protein DNA polymerase III subunit delta / DNA polymerase III holoenzyme


Mass: 38745.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: holA, b0640, JW0635 / Production host: Escherichia coli (E. coli) / References: UniProt: P28630, DNA-directed DNA polymerase
#2: Protein
DNA polymerase III subunit tau / DNA polymerase III holoenzyme / DNA polymerase III subunit gamma


Mass: 43955.512 Da / Num. of mol.: 6 / Fragment: UNP residues 1-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: dnaX, dnaZ, dnaZX, b0470, JW0459 / Production host: Escherichia coli (E. coli) / References: UniProt: P06710, DNA-directed DNA polymerase
#3: Protein DNA polymerase III subunit delta' / DNA polymerase III holoenzyme


Mass: 36980.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: holB, b1099, JW1085 / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase

-
DNA chain , 2 types, 4 molecules KMLN

#4: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3')


Mass: 4589.994 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: DNA chain DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')


Mass: 3019.991 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Non-polymers , 4 types, 26 molecules

#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: BeF3
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 9% PEG 400, 150 mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2HEPES12
3PEG 40012
4MgCl212

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2008
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.388→50 Å / Num. all: 84294 / Num. obs: 83114 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.388→3.52 Å / % possible all: 94.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.388→49.97 Å / SU ML: 0.36 / σ(F): 1.33 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 4165 5.04 %Random
Rwork0.2214 ---
obs0.2234 82646 97.47 %-
all-82646 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.958 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5959 Å20 Å20 Å2
2--0.3842 Å2-0 Å2
3----3.9801 Å2
Refinement stepCycle: LAST / Resolution: 3.388→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27584 974 200 0 28758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01729418
X-RAY DIFFRACTIONf_angle_d1.81340191
X-RAY DIFFRACTIONf_dihedral_angle_d19.80511051
X-RAY DIFFRACTIONf_chiral_restr0.14625
X-RAY DIFFRACTIONf_plane_restr0.0075013
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2871X-RAY DIFFRACTIONPOSITIONAL
12H2871X-RAY DIFFRACTIONPOSITIONAL0.079
21D2851X-RAY DIFFRACTIONPOSITIONAL
22I2851X-RAY DIFFRACTIONPOSITIONAL0.1
31B2862X-RAY DIFFRACTIONPOSITIONAL
32G2862X-RAY DIFFRACTIONPOSITIONAL0.073
41E2602X-RAY DIFFRACTIONPOSITIONAL
42J2602X-RAY DIFFRACTIONPOSITIONAL0.091
51A2650X-RAY DIFFRACTIONPOSITIONAL
52F2650X-RAY DIFFRACTIONPOSITIONAL0.073
61K487X-RAY DIFFRACTIONPOSITIONAL
62M487X-RAY DIFFRACTIONPOSITIONAL0.085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.388-3.42620.30591070.31041897X-RAY DIFFRACTION72
3.4262-3.46650.35981130.30512528X-RAY DIFFRACTION93
3.4665-3.50880.34421260.29342526X-RAY DIFFRACTION96
3.5088-3.55320.31211330.28612540X-RAY DIFFRACTION95
3.5532-3.59990.32531290.27622526X-RAY DIFFRACTION95
3.5999-3.64920.28621470.28332552X-RAY DIFFRACTION97
3.6492-3.70130.32581450.27432575X-RAY DIFFRACTION97
3.7013-3.75660.31291450.25632574X-RAY DIFFRACTION98
3.7566-3.81530.30091330.26042610X-RAY DIFFRACTION98
3.8153-3.87780.32111240.2572647X-RAY DIFFRACTION98
3.8778-3.94460.32561430.25392580X-RAY DIFFRACTION98
3.9446-4.01630.2871410.24322642X-RAY DIFFRACTION99
4.0163-4.09350.28931370.2342636X-RAY DIFFRACTION99
4.0935-4.1770.26611410.24282640X-RAY DIFFRACTION99
4.177-4.26780.27711420.22342590X-RAY DIFFRACTION99
4.2678-4.3670.28831470.21482640X-RAY DIFFRACTION98
4.367-4.47620.25711310.20472642X-RAY DIFFRACTION99
4.4762-4.59710.24731560.1962613X-RAY DIFFRACTION98
4.5971-4.73230.22661250.19952647X-RAY DIFFRACTION99
4.7323-4.88490.21711380.18982649X-RAY DIFFRACTION99
4.8849-5.05940.24811370.192675X-RAY DIFFRACTION99
5.0594-5.26170.25621180.19152704X-RAY DIFFRACTION100
5.2617-5.50090.25141420.19932697X-RAY DIFFRACTION100
5.5009-5.79050.25871430.19922673X-RAY DIFFRACTION100
5.7905-6.15270.26041570.19682685X-RAY DIFFRACTION100
6.1527-6.62680.25371540.20192722X-RAY DIFFRACTION100
6.6268-7.29180.22121510.18512705X-RAY DIFFRACTION100
7.2918-8.34270.19561640.14542720X-RAY DIFFRACTION100
8.3427-10.49490.13111370.12542781X-RAY DIFFRACTION100
10.4949-49.97510.2121590.20222865X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.81740.64070.09822.62352.78842.70660.177-0.6549-0.60650.7816-0.61920.43560.6868-0.7543-01.18420.0619-0.2261.3611-0.19831.38147.545720.347150.3361
23.76991.2467-0.13573.1662-0.15612.3248-0.1013-0.10260.6036-0.2931-0.14550.0668-0.643-0.1726-00.91920.1367-0.17130.6583-0.14910.958636.035539.532249.8897
34.4994-1.2117-0.12831.42780.88451.3415-0.05450.0370.282-0.36350.0773-0.592-0.39790.577600.6204-0.21030.09910.9188-0.12870.940867.189425.764647.9033
41.2212-0.2496-0.01513.63630.54662.8077-0.0498-0.1239-0.27520.30950.2742-0.71570.50890.607500.55620.164-0.03090.9096-0.29081.006272.5665-8.18648.5473
51.57681.34221.39842.72731.84232.10020.0545-0.3023-0.04560.76930.12320.00450.8509-0.0113-01.19720.0505-0.0010.6567-0.04920.650149.7667-27.590347.1284
61.54541.06382.11211.8051-0.65642.44890.0110.70580.8564-0.1477-0.0569-0.507-0.79211.042701.3924-0.00550.04631.12750.12921.643511.86322.6286-43.8695
72.53041.6824-0.55242.4659-1.06192.5385-0.0850.13680.427-0.1940.02590.6888-0.3287-0.491800.77650.16950.04510.72940.04711.0693-16.3719-0.4149-44.9358
81.5618-0.42360.55935.6681-1.01641.9899-0.1580.0049-0.0144-0.12660.1880.47460.0155-0.357100.5263-0.06190.08210.59960.08390.5172-12.0368-32.9925-43.3236
93.7778-0.87641.07741.53450.11013.08570.13480.1111-0.4014-0.0064-0.0738-0.15980.45110.1655-00.7061-0.00590.13060.43960.0860.492518.2961-48.9117-43.2048
103.57831.2451.26751.65980.84362.76250.01650.41770.0854-0.31840.0525-0.40510.36880.762700.61450.04330.19360.84450.0960.666443.7958-33.9876-40.537
111.93570.0929-0.18842.53990.47461.9165-0.00210.15870.3603-0.35410.1058-0.4565-0.3810.5835-00.812-0.02130.00760.9076-0.09230.654848.8495-2.637317.6226
121.5762-0.08470.55572.469-0.16240.8182-0.0137-0.1919-0.00470.2660.04650.2471-0.0752-0.1946-00.69790.01910.09210.72370.03420.47319.6274-25.1564-12.015
130.2619-0.6357-0.42042.46880.59320.23060.69060.3095-0.1094-0.10330.07750.38410.3862-1.2566-00.8790.0606-0.04661.1072-0.18050.684437.51966.152351.7257
142.5429-1.94830.51480.2961-1.32380.27440.10420.16260.52460.34960.4637-0.2499-0.78070.978801.1386-0.117-0.02610.78320.09150.647716.032-11.1313-46.1364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 1:211A1 - 211
2X-RAY DIFFRACTION2(chain B and resseq 5:246) or (chain B and (resseq 400:403))B5 - 246
3X-RAY DIFFRACTION2(chain B and resseq 5:246) or (chain B and (resseq 400:403))B400 - 403
4X-RAY DIFFRACTION3(chain C and resseq 4:246) or (chain C and (resseq 400:403))C4 - 246
5X-RAY DIFFRACTION3(chain C and resseq 4:246) or (chain C and (resseq 400:403))C400 - 403
6X-RAY DIFFRACTION4(chain D and resseq 2:246) or (chain D and (resseq 400:403))D2 - 246
7X-RAY DIFFRACTION4(chain D and resseq 2:246) or (chain D and (resseq 400:403))D400 - 403
8X-RAY DIFFRACTION5(chain E and resseq 1:207) or (chain E and resseq 403)E1 - 207
9X-RAY DIFFRACTION5(chain E and resseq 1:207) or (chain E and resseq 403)E403
10X-RAY DIFFRACTION6chain F and resseq 1:211F1 - 211
11X-RAY DIFFRACTION7(chain G and resseq -9:246) or (chain G and (resseq 400:403))G-9 - 246
12X-RAY DIFFRACTION7(chain G and resseq -9:246) or (chain G and (resseq 400:403))G400 - 403
13X-RAY DIFFRACTION8(chain H and resseq 4:246) or (chain H and (resseq 400:403))H4 - 246
14X-RAY DIFFRACTION8(chain H and resseq 4:246) or (chain H and (resseq 400:403))H400 - 403
15X-RAY DIFFRACTION9(chain I and resseq 2:246) or (chain I and (resseq 400:403))I2 - 246
16X-RAY DIFFRACTION9(chain I and resseq 2:246) or (chain I and (resseq 400:403))I400 - 403
17X-RAY DIFFRACTION10(chain J and resseq 1:207) or (chain J and resseq 403)J1 - 207
18X-RAY DIFFRACTION10(chain J and resseq 1:207) or (chain J and resseq 403)J403
19X-RAY DIFFRACTION11(chain A and resseq 212:333) or (chain B and resseq 247:368) or (chain C and resseq 247:368) or (chain D and resseq 247:363) or (chain E and resseq 208:334)A212 - 333
20X-RAY DIFFRACTION11(chain A and resseq 212:333) or (chain B and resseq 247:368) or (chain C and resseq 247:368) or (chain D and resseq 247:363) or (chain E and resseq 208:334)B247 - 368
21X-RAY DIFFRACTION11(chain A and resseq 212:333) or (chain B and resseq 247:368) or (chain C and resseq 247:368) or (chain D and resseq 247:363) or (chain E and resseq 208:334)C247 - 368
22X-RAY DIFFRACTION11(chain A and resseq 212:333) or (chain B and resseq 247:368) or (chain C and resseq 247:368) or (chain D and resseq 247:363) or (chain E and resseq 208:334)D247 - 363
23X-RAY DIFFRACTION11(chain A and resseq 212:333) or (chain B and resseq 247:368) or (chain C and resseq 247:368) or (chain D and resseq 247:363) or (chain E and resseq 208:334)E208 - 334
24X-RAY DIFFRACTION12(chain F and resseq 212:333) or (chain G and resseq 247:368) or (chain H and resseq 247:368) or (chain I and resseq 247:363) or (chain J and resseq 208:334)F212 - 333
25X-RAY DIFFRACTION12(chain F and resseq 212:333) or (chain G and resseq 247:368) or (chain H and resseq 247:368) or (chain I and resseq 247:363) or (chain J and resseq 208:334)G247 - 368
26X-RAY DIFFRACTION12(chain F and resseq 212:333) or (chain G and resseq 247:368) or (chain H and resseq 247:368) or (chain I and resseq 247:363) or (chain J and resseq 208:334)H247 - 368
27X-RAY DIFFRACTION12(chain F and resseq 212:333) or (chain G and resseq 247:368) or (chain H and resseq 247:368) or (chain I and resseq 247:363) or (chain J and resseq 208:334)I247 - 363
28X-RAY DIFFRACTION12(chain F and resseq 212:333) or (chain G and resseq 247:368) or (chain H and resseq 247:368) or (chain I and resseq 247:363) or (chain J and resseq 208:334)J208 - 334
29X-RAY DIFFRACTION13chain K or chain LK2 - 15
30X-RAY DIFFRACTION13chain K or chain LL1 - 10
31X-RAY DIFFRACTION14chain M or chain NM2 - 15
32X-RAY DIFFRACTION14chain M or chain NN1 - 10

+
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