[English] 日本語
Yorodumi
- PDB-4poq: Structure of unliganded VP1 pentamer of Human Polyomavirus 9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4poq
TitleStructure of unliganded VP1 pentamer of Human Polyomavirus 9
ComponentsVP1
KeywordsVIRAL PROTEIN / jelly roll fold / capsid formation / receptor interaction / carbohydrate / sialyloligosaccharide / viral coat protein
Function / homology
Function and homology information


T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Capsid protein VP1
Similarity search - Component
Biological speciesHuman polyomavirus 9
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKhan, Z.M. / Stehle, T.
CitationJournal: J.Virol. / Year: 2014
Title: Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate.
Authors: Khan, Z.M. / Liu, Y. / Neu, U. / Gilbert, M. / Ehlers, B. / Feizi, T. / Stehle, T.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_label_asym_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,26441
Polymers301,58010
Non-polymers1,68431
Water33,9581885
1
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,60120
Polymers150,7905
Non-polymers81115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23960 Å2
ΔGint-172 kcal/mol
Surface area49420 Å2
MethodPISA
2
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,66321
Polymers150,7905
Non-polymers87316
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24230 Å2
ΔGint-172 kcal/mol
Surface area50320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.330, 180.090, 199.390
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
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA46 - 5220 - 26
21THRTHRLEULEUBB46 - 5220 - 26
31THRTHRLEULEUCC46 - 5220 - 26
41THRTHRLEULEUDD46 - 5220 - 26
51THRTHRLEULEUEE46 - 5220 - 26
61THRTHRLEULEUFF46 - 5220 - 26
71THRTHRLEULEUGG46 - 5220 - 26
81THRTHRLEULEUHH46 - 5220 - 26
91THRTHRLEULEUII46 - 5220 - 26
101THRTHRLEULEUJJ46 - 5220 - 26
12GLYGLYGLYGLYAA140 - 160114 - 134
22GLYGLYGLYGLYBB140 - 160114 - 134
32GLYGLYGLYGLYCC140 - 160114 - 134
42GLYGLYGLYGLYDD140 - 160114 - 134
52GLYGLYGLYGLYEE140 - 160114 - 134
62GLYGLYGLYGLYFF140 - 160114 - 134
72GLYGLYGLYGLYGG140 - 160114 - 134
82GLYGLYGLYGLYHH140 - 160114 - 134
92GLYGLYGLYGLYII140 - 160114 - 134
102GLYGLYGLYGLYJJ140 - 160114 - 134
13ASPASPVALVALAA250 - 268224 - 242
23ASPASPVALVALBB250 - 268224 - 242
33ASPASPVALVALCC250 - 268224 - 242
43ASPASPVALVALDD250 - 268224 - 242
53ASPASPVALVALEE250 - 268224 - 242
63ASPASPVALVALFF250 - 268224 - 242
73ASPASPVALVALGG250 - 268224 - 242
83ASPASPVALVALHH250 - 268224 - 242
93ASPASPVALVALII250 - 268224 - 242
103ASPASPVALVALJJ250 - 268224 - 242
14SERSERPROPROAA280 - 287254 - 261
24SERSERPROPROBB280 - 287254 - 261
34SERSERPROPROCC280 - 287254 - 261
44SERSERPROPRODD280 - 287254 - 261
54SERSERPROPROEE280 - 287254 - 261
64SERSERPROPROFF280 - 287254 - 261
74SERSERPROPROGG280 - 287254 - 261
84SERSERPROPROHH280 - 287254 - 261
94SERSERPROPROII280 - 287254 - 261
104SERSERPROPROJJ280 - 287254 - 261

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.311856, 0.743323, -0.591791), (-0.67947, 0.609843, 0.407937), (0.664128, 0.274886, 0.695249)18.17857, 19.35775, -18.60084
3given(-0.801567, 0.519184, -0.296545), (-0.356305, -0.016493, 0.934224), (0.480143, 0.854503, 0.198208)48.90553, 11.35452, -14.36818
4given(-0.800729, -0.356638, 0.481292), (0.517295, -0.006537, 0.855782), (-0.302058, 0.93422, 0.189721)50.12475, -12.16757, 6.5441
5given(0.321729, -0.669427, 0.669595), (0.734582, 0.622675, 0.269565), (-0.597394, 0.405145, 0.692082)20.39319, -19.32134, 15.66247
6given(-0.860804, -0.393938, 0.322225), (-0.379875, 0.075989, -0.921911), (0.33869, -0.915991, -0.215059)45.6924, -43.61626, -70.55515
7given(-0.759992, 0.470383, -0.4485), (0.478349, -0.062341, -0.875954), (-0.439993, -0.880258, -0.177628)41.89611, -66.9454, -49.39714
8given(0.370877, 0.629976, -0.682335), (0.631193, -0.709938, -0.312382), (-0.681209, -0.31483, -0.660936)10.91298, -70.36228, -43.57854
9given(0.987808, -0.148194, -0.047679), (-0.148331, -0.988938, 0.00068), (-0.047252, 0.006401, -0.998862)-4.87074, -48.65557, -61.28099
10given(0.234031, -0.781369, 0.578525), (-0.777737, -0.507529, -0.370863), (0.5834, -0.363147, -0.726477)16.58786, -32.27698, -77.82615

-
Components

#1: Protein
VP1 / Major Capsid Protein


Mass: 30157.977 Da / Num. of mol.: 10 / Fragment: UNP residues 32-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human polyomavirus 9 / Gene: gp3, vp1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9NQ90
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1885 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.15
Details: 20% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2012 / Details: mirrors
RadiationMonochromator: channel cut ESRF Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→133.647 Å / Num. all: 226820 / Num. obs: 235836 / % possible obs: 96.17 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.54 % / Biso Wilson estimate: 30.38 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.14
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.1 / Num. unique all: 16603 / % possible all: 95.92

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.8.0025refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MBX
Resolution: 2→133.647 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.747 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23556 11393 5 %RANDOM
Rwork0.19636 ---
all0.19834 226820 --
obs0.19834 215427 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.728 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å2-0 Å2-0 Å2
2--0.28 Å2-0 Å2
3----3.31 Å2
Refinement stepCycle: LAST / Resolution: 2→133.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20697 0 94 1885 22676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221348
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.97629150
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21652740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09125.561856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.632153484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0861572
X-RAY DIFFRACTIONr_chiral_restr0.0790.23390
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116074
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7321.53210891
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.262.57613609
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0231.64910457
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.6336.36434073
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A214MEDIUM POSITIONAL0.090.5
2B214MEDIUM POSITIONAL0.10.5
3C214MEDIUM POSITIONAL0.090.5
4D214MEDIUM POSITIONAL0.10.5
5E214MEDIUM POSITIONAL0.10.5
6F214MEDIUM POSITIONAL0.130.5
7G214MEDIUM POSITIONAL0.120.5
8H214MEDIUM POSITIONAL0.110.5
9I214MEDIUM POSITIONAL0.080.5
10J214MEDIUM POSITIONAL0.140.5
1A168LOOSE POSITIONAL0.335
2B168LOOSE POSITIONAL0.275
3C168LOOSE POSITIONAL0.215
4D168LOOSE POSITIONAL0.195
5E168LOOSE POSITIONAL0.255
6F168LOOSE POSITIONAL0.235
7G168LOOSE POSITIONAL0.225
8H168LOOSE POSITIONAL0.45
9I168LOOSE POSITIONAL0.275
10J168LOOSE POSITIONAL0.265
1A214MEDIUM THERMAL1.452
2B214MEDIUM THERMAL0.962
3C214MEDIUM THERMAL1.142
4D214MEDIUM THERMAL1.012
5E214MEDIUM THERMAL0.872
6F214MEDIUM THERMAL1.92
7G214MEDIUM THERMAL1.112
8H214MEDIUM THERMAL1.332
9I214MEDIUM THERMAL1.032
10J214MEDIUM THERMAL1.292
1A168LOOSE THERMAL1.610
2B168LOOSE THERMAL1.3410
3C168LOOSE THERMAL1.4910
4D168LOOSE THERMAL1.5210
5E168LOOSE THERMAL1.0610
6F168LOOSE THERMAL2.5510
7G168LOOSE THERMAL1.6110
8H168LOOSE THERMAL1.910
9I168LOOSE THERMAL1.2810
10J168LOOSE THERMAL2.0110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 866 -
Rwork0.286 15697 -
obs-15697 95.72 %
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)
10.3993-0.11850.09671.79711.28032.3158-0.0473-0.01020.058-0.06970.1882-0.1766-0.17040.4735-0.14080.0449-0.00780.01220.1282-0.01080.246553.1843-46.6434-57.5989
20.2159-0.1583-0.04010.28690.12920.47430.00160.02350.0121-0.04550.0622-0.09550.03890.1445-0.06380.08980.0125-0.0080.074-0.01830.231443.0825-51.654-62.9719
30.42080.0535-0.01611.14670.39680.9281-0.0172-0.0596-0.00370.09360.0583-0.10430.06850.1378-0.04110.05210.0385-0.00870.0439-0.0070.19946.4004-50.2316-54.0946
40.79110.47910.32531.48871.62242.8471-0.0423-0.03150.1326-0.22290.0370.0089-0.23570.09210.00530.1001-0.0013-0.00570.020.04140.203729.6256-25.324-75.098
50.4452-0.01840.01970.60380.3570.64030.00020.02780.0461-0.1443-0.0051-0.0019-0.05780.01760.00490.06750.0062-0.010.00580.02170.190231.0195-36.031-72.7989
60.65910.85870.4663.84252.72222.80130.0219-0.0430.0527-0.04790.0251-0.0636-0.05350.1213-0.0470.03230.0036-0.01070.02120.01550.178228.3721-27.6472-68.5446
70.31750.24720.23112.05011.47972.43170.0273-0.00760.0709-0.0228-0.21190.3252-0.0812-0.42710.18460.01640.017-0.04690.1837-0.02970.3439-3.3134-35.3572-64.9485
80.4003-0.4585-0.31823.39851.41651.3551-0.0019-0.002-0.0052-0.0058-0.09470.21030.0659-0.24210.09670.0205-0.0391-0.02230.0977-0.01460.25573.2144-46.4541-60.6679
90.3402-0.1527-0.28590.60080.47591.40890.03020.03060.0525-0.0667-0.10050.1461-0.1165-0.22620.07020.03680.0179-0.04670.0799-0.02080.26224.891-34.319-66.8909
100.8618-0.09190.06881.33821.05081.049-0.0178-0.105-0.08020.185-0.04580.130.1334-0.180.06350.1979-0.11460.06050.17280.01930.3295-0.8267-61.0296-40.4945
110.10240.0008-0.09850.28960.08560.59790.0114-0.031-0.03970.0916-0.05040.14310.1352-0.2080.0390.1052-0.08840.02230.135-0.03430.30743.1419-58.3456-50.4169
120.4961-0.667-0.66792.18962.11413.1341-0.0297-0.0019-0.01430.0909-0.11140.21530.1137-0.29170.14120.0929-0.08680.02920.1125-0.00590.2763.5073-55.8976-40.7863
130.77440.0123-0.42291.71810.90571.63850.0244-0.1894-0.02260.38650.0723-0.10090.37880.2029-0.09680.22520.0259-0.02930.06080.03790.231134.1683-68.622-35.8543
140.4455-0.0508-0.00410.32960.04480.55320.0313-0.0615-0.07490.1389-0.02930.02170.2352-0.0509-0.0020.186-0.02840.00410.02220.00560.215926.8931-67.3457-45.1321
150.51840.0083-0.31.95462.08083.75870.0347-0.09770.0160.1539-0.05230.00820.1226-0.12520.01760.11440.0032-0.00720.03460.01130.193332.071-62.3501-37.9727
160.1651-0.1659-0.19094.80353.11022.85990.01430.0432-0.0239-0.2043-0.25680.3945-0.1743-0.45590.24240.0723-0.03190.06510.185-0.02870.364-1.9791-13.1831-2.826
170.27910.13630.16281.48610.57540.52130.0164-0.0878-0.01280.0981-0.05830.11870.0232-0.17920.0420.11620.00420.06460.1026-0.0080.27754.7342-9.16823.1466
180.35960.20720.3750.57250.23360.61860.0274-0.0697-0.03580.1879-0.05420.1250.1597-0.12180.02680.1375-0.02890.08450.0996-0.01570.28947.5705-15.86764.9414
190.88170.56780.73472.23851.70512.0346-0.05940.03440.062-0.1706-0.02530.1597-0.2087-0.13930.08470.09350.07430.00370.07880.01540.30064.842411.4983-21.1199
200.23520.05850.18110.14560.14960.6424-0.0207-0.04080.0360.013-0.01630.1265-0.1089-0.15080.0370.09780.0390.02260.0573-0.03030.30518.76138.2914-11.2631
210.59980.82731.10792.15611.95022.7290.0417-0.0704-0.03320.0627-0.08010.17-0.0276-0.18220.03840.05990.03850.01730.049-0.00950.25128.60615.6818-21.1043
220.71430.38160.68121.74791.33982.3637-0.05110.14510.0005-0.2030.1454-0.0631-0.2650.2729-0.09430.106-0.05450.01820.05340.01480.218240.184614.211-26.9919
230.4086-0.06260.04820.28990.03660.8612-0.00180.02030.04690.0186-0.00360.0205-0.20170.03840.00540.1037-0.01890.00380.0052-0.01050.218333.24513.7291-17.8917
240.81820.29690.7231.87512.82445.76060.00580.05930.0002-0.10720.01050.0385-0.245-0.0109-0.01630.0275-0.00260.00740.00930.00730.185137.09098.3161-26.3976
250.31960.210.12021.94631.61262.9542-0.01990.0314-0.04530.05390.1884-0.19440.19170.4055-0.16850.05220.011-0.04170.1377-0.02580.297556.9482-10.5857-6.9242
260.2094-0.16160.00220.64040.18250.7397-0.0179-0.0238-0.00410.1090.0547-0.11370.02830.1506-0.03690.0882-0.0123-0.0240.0607-0.02660.221848.8729-2.501-4.9798
270.6763-0.166-0.58922.34062.37694.10220.03020.0339-0.0093-0.04240.0501-0.1135-0.05610.1006-0.08030.040.0181-0.04410.03250.01010.20450.5273-11.4286-8.67
280.4981-0.2455-0.03912.01281.61832.5505-0.0285-0.0169-0.14210.2289-0.00730.03410.2521-0.02970.03580.21980.00090.01210.0760.03470.236831.6207-28.715211.6473
290.4786-0.0717-0.03290.41640.10220.54090.0079-0.0775-0.020.18960.0003-0.01170.11370.0289-0.00820.17510.01340.00050.05040.00070.212734.0791-17.95619.7245
300.463-0.3376-0.1433.02912.1062.49140.00350.0336-0.04750.06230.0285-0.02810.10940.1035-0.03210.1434-0.00160.01880.0360.01770.184830.829-26.99325.497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 109
2X-RAY DIFFRACTION2A110 - 183
3X-RAY DIFFRACTION3A184 - 303
4X-RAY DIFFRACTION4B34 - 108
5X-RAY DIFFRACTION5B109 - 245
6X-RAY DIFFRACTION6B246 - 302
7X-RAY DIFFRACTION7C34 - 106
8X-RAY DIFFRACTION8C107 - 158
9X-RAY DIFFRACTION9C159 - 302
10X-RAY DIFFRACTION10D34 - 108
11X-RAY DIFFRACTION11D109 - 246
12X-RAY DIFFRACTION12D247 - 303
13X-RAY DIFFRACTION13E34 - 110
14X-RAY DIFFRACTION14E111 - 245
15X-RAY DIFFRACTION15E246 - 302
16X-RAY DIFFRACTION16F34 - 70
17X-RAY DIFFRACTION17F71 - 165
18X-RAY DIFFRACTION18F166 - 304
19X-RAY DIFFRACTION19G34 - 108
20X-RAY DIFFRACTION20G109 - 245
21X-RAY DIFFRACTION21G246 - 303
22X-RAY DIFFRACTION22H34 - 109
23X-RAY DIFFRACTION23H110 - 245
24X-RAY DIFFRACTION24H246 - 304
25X-RAY DIFFRACTION25I32 - 109
26X-RAY DIFFRACTION26I110 - 246
27X-RAY DIFFRACTION27I247 - 302
28X-RAY DIFFRACTION28J32 - 108
29X-RAY DIFFRACTION29J109 - 246
30X-RAY DIFFRACTION30J247 - 304

+
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