[English] 日本語
Yorodumi
- PDB-5ejb: Crystal structure of prefusion Hendra virus F protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ejb
TitleCrystal structure of prefusion Hendra virus F protein
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / prefusion form / viral glycoprotein / ectodomain
Function / homology
Function and homology information


host cell surface / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHendra virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWong, J.W. / Jardetzky, T.S. / Paterson, R.G. / Lamb, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-61050 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure and stabilization of the Hendra virus F glycoprotein in its prefusion form.
Authors: Wong, J.J. / Paterson, R.G. / Lamb, R.A. / Jardetzky, T.S.
History
DepositionNov 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references / Derived calculations
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
D: Fusion glycoprotein F0
F: Fusion glycoprotein F0
E: Fusion glycoprotein F0
A: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,50627
Polymers331,0026
Non-polymers4,50421
Water00
1
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
A: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,30211
Polymers165,5013
Non-polymers1,8018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Fusion glycoprotein F0
F: Fusion glycoprotein F0
E: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,20416
Polymers165,5013
Non-polymers2,70313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.610, 163.500, 147.940
Angle α, β, γ (deg.)90.000, 94.130, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F
13A
23B
33C
43D
53E
63F
14A
24B
34C
44D
54E
64F
15A
25B
35C
45D
55E
65F
16A
26C
36E
46F
17B
27C
37E
18A
28B
38C
48D
58E
68F
19A
29B
39C
49D
59E
69F
110A
210B
310C
410D
510E
610F
111A
211B
311C
411D
511E
611F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLYSLYS1AF29 - 494 - 24
21HISHISLYSLYS1BA29 - 494 - 24
31HISHISLYSLYS1CB29 - 494 - 24
41HISHISLYSLYS1DC29 - 494 - 24
51HISHISLYSLYS1EE29 - 494 - 24
61HISHISLYSLYS1FD29 - 494 - 24
12THRTHRPROPRO1AF54 - 6329 - 38
22THRTHRPROPRO1BA54 - 6329 - 38
32THRTHRPROPRO1CB54 - 6329 - 38
42THRTHRPROPRO1DC54 - 6329 - 38
52THRTHRPROPRO1EE54 - 6329 - 38
62THRTHRPROPRO1FD54 - 6329 - 38
13METMETASNASN1AF76 - 9851 - 73
23METMETASNASN1BA76 - 9851 - 73
33METMETASNASN1CB76 - 9851 - 73
43METMETASNASN1DC76 - 9851 - 73
53METMETASNASN1EE76 - 9851 - 73
63METMETASNASN1FD76 - 9851 - 73
14GLUGLULEULEU1AF196 - 246171 - 221
24GLUGLULEULEU1BA196 - 246171 - 221
34GLUGLULEULEU1CB196 - 246171 - 221
44GLUGLULEULEU1DC196 - 246171 - 221
54GLUGLULEULEU1EE196 - 246171 - 221
64GLUGLULEULEU1FD196 - 246171 - 221
15PHEPHEASPASP1AF253 - 413228 - 388
25PHEPHEASPASP1BA253 - 413228 - 388
35PHEPHEASPASP1CB253 - 413228 - 388
45PHEPHEASPASP1DC253 - 413228 - 388
55PHEPHEASPASP1EE253 - 413228 - 388
65PHEPHEASPASP1FD253 - 413228 - 388
16SERSERLEULEU2AF50 - 5325 - 28
26SERSERLEULEU2CB50 - 5325 - 28
36SERSERLEULEU2EE50 - 5325 - 28
46SERSERLEULEU2FD50 - 5325 - 28
17LEULEUTHRTHR6BA183 - 195158 - 170
27LEULEUTHRTHR6CB183 - 195158 - 170
37LEULEUTHRTHR6EE183 - 195158 - 170
18ASNASNASNASN1AF100 - 18275 - 157
28ASNASNASNASN1BA100 - 18275 - 157
38ASNASNASNASN1CB100 - 18275 - 157
48ASNASNASNASN1DC100 - 18275 - 157
58ASNASNASNASN1EE100 - 18275 - 157
68ASNASNASNASN1FD100 - 18275 - 157
19THRTHRMETMET1AF415 - 463390 - 438
29THRTHRMETMET1BA415 - 463390 - 438
39THRTHRMETMET1CB415 - 463390 - 438
49THRTHRMETMET1DC415 - 463390 - 438
59THRTHRMETMET1EE415 - 463390 - 438
69THRTHRMETMET1FD415 - 463390 - 438
110GLNGLNGLUGLU1AF465 - 476440 - 451
210GLNGLNGLUGLU1BA465 - 476440 - 451
310GLNGLNGLUGLU1CB465 - 476440 - 451
410GLNGLNGLUGLU1DC465 - 476440 - 451
510GLNGLNGLUGLU1EE465 - 476440 - 451
610GLNGLNGLUGLU1FD465 - 476440 - 451
111ASNASNVALVAL4AF64 - 7539 - 50
211ASNASNVALVAL4BA64 - 7539 - 50
311ASNASNVALVAL4CB64 - 7539 - 50
411ASNASNVALVAL4DC64 - 7539 - 50
511ASNASNVALVAL4EE64 - 7539 - 50
611ASNASNVALVAL4FD64 - 7539 - 50

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

-
Components

#1: Protein
Fusion glycoprotein F0


Mass: 55166.992 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hendra virus / Gene: F / Plasmid: pCAGGS3 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: O89342*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100mM sodium acetate pH 5.0, 1.75M lithium sulfate, 100mM magnesium sulfate, 3.4 % isopropanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99969 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2014
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99969 Å / Relative weight: 1
ReflectionResolution: 3.2→49.62 Å / Num. obs: 80411 / % possible obs: 99.63 % / Redundancy: 3.99 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.37
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 4.07 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.9 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSJanuary 10, 2014data scaling
MOLREPphasing
XDSJanuary 10, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B9B

2b9b


Resolution: 3.2→49.62 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.887 / SU B: 59.64 / SU ML: 0.452 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2833 4233 5 %RANDOM
Rwork0.2527 ---
obs0.2542 80411 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.64 Å2 / Biso mean: 95.232 Å2 / Biso min: 38.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å22.35 Å2
2--2.39 Å20 Å2
3----5.11 Å2
Refinement stepCycle: final / Resolution: 3.2→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20133 0 282 0 20415
Biso mean--118.07 --
Num. residues----2673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0220759
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.98728290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75752657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76926.057776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.092153508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7651554
X-RAY DIFFRACTIONr_chiral_restr0.0990.23534
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115021
X-RAY DIFFRACTIONr_mcbond_it3.0284.36310676
X-RAY DIFFRACTIONr_mcangle_it5.0976.52913317
X-RAY DIFFRACTIONr_scbond_it4.0914.81410083
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A102TIGHT POSITIONAL0.030.05
12B102TIGHT POSITIONAL0.030.05
13C102TIGHT POSITIONAL0.030.05
14D102TIGHT POSITIONAL0.020.05
15E102TIGHT POSITIONAL0.020.05
16F102TIGHT POSITIONAL0.020.05
11A172TIGHT THERMAL7.320.5
12B172TIGHT THERMAL6.990.5
13C172TIGHT THERMAL4.690.5
14D172TIGHT THERMAL5.160.5
15E172TIGHT THERMAL3.720.5
16F172TIGHT THERMAL6.230.5
21A76TIGHT THERMAL4.310.5
22B76TIGHT THERMAL7.690.5
23C76TIGHT THERMAL8.270.5
24D76TIGHT THERMAL4.450.5
25E76TIGHT THERMAL5.520.5
26F76TIGHT THERMAL3.750.5
31A182TIGHT THERMAL7.510.5
32B182TIGHT THERMAL8.670.5
33C182TIGHT THERMAL8.60.5
34D182TIGHT THERMAL6.530.5
35E182TIGHT THERMAL5.070.5
36F182TIGHT THERMAL6.370.5
41A393TIGHT THERMAL8.830.5
42B393TIGHT THERMAL8.880.5
43C393TIGHT THERMAL7.640.5
44D393TIGHT THERMAL9.570.5
45E393TIGHT THERMAL6.690.5
46F393TIGHT THERMAL8.660.5
51A1249TIGHT THERMAL7.340.5
52B1249TIGHT THERMAL9.460.5
53C1249TIGHT THERMAL6.830.5
54D1249TIGHT THERMAL8.620.5
55E1249TIGHT THERMAL7.250.5
56F1249TIGHT THERMAL7.820.5
61A13MEDIUM POSITIONAL0.050.5
62C13MEDIUM POSITIONAL0.040.5
63E13MEDIUM POSITIONAL0.050.5
64F13MEDIUM POSITIONAL0.040.5
61A16TIGHT THERMAL8.670.5
62C16TIGHT THERMAL9.60.5
63E16TIGHT THERMAL7.080.5
64F16TIGHT THERMAL5.830.5
61A13MEDIUM THERMAL12.352
62C13MEDIUM THERMAL18.052
63E13MEDIUM THERMAL5.442
64F13MEDIUM THERMAL9.512
71B98LOOSE POSITIONAL0.785
72C98LOOSE POSITIONAL0.585
73E98LOOSE POSITIONAL0.675
71B98LOOSE THERMAL5.7310
72C98LOOSE THERMAL3.110
73E98LOOSE THERMAL5.5510
81A517TIGHT THERMAL5.730.5
82B517TIGHT THERMAL8.030.5
83C517TIGHT THERMAL8.780.5
84D517TIGHT THERMAL7.970.5
85E517TIGHT THERMAL9.460.5
86F517TIGHT THERMAL6.60.5
91A340TIGHT THERMAL8.840.5
92B340TIGHT THERMAL12.490.5
93C340TIGHT THERMAL11.370.5
94D340TIGHT THERMAL9.860.5
95E340TIGHT THERMAL90.5
96F340TIGHT THERMAL12.10.5
101A102TIGHT THERMAL19.470.5
102B102TIGHT THERMAL10.490.5
103C102TIGHT THERMAL13.70.5
104D102TIGHT THERMAL18.030.5
105E102TIGHT THERMAL12.870.5
106F102TIGHT THERMAL11.480.5
111A82MEDIUM POSITIONAL0.570.5
112B82MEDIUM POSITIONAL0.560.5
113C82MEDIUM POSITIONAL0.520.5
114D82MEDIUM POSITIONAL0.690.5
115E82MEDIUM POSITIONAL0.490.5
116F82MEDIUM POSITIONAL0.510.5
111A82MEDIUM THERMAL13.62
112B82MEDIUM THERMAL12.12
113C82MEDIUM THERMAL7.632
114D82MEDIUM THERMAL7.352
115E82MEDIUM THERMAL5.982
116F82MEDIUM THERMAL7.382
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 312 -
Rwork0.36 5928 -
all-6240 -
obs--99.78 %
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)
12.0997-0.1001-0.12021.03820.07254.348-0.072-0.0289-0.1153-0.2142-0.0784-0.27720.24350.87080.15050.64690.0586-0.17070.19920.05650.192367.636-6.03521.535
20.1850.39060.07242.00651.53395.0377-0.0953-0.1395-0.11920.1148-0.1076-0.20780.37520.40070.20290.90670.0529-0.12920.18560.08370.22154.708-7.9150.483
32.5180.19190.05012.50711.29623.18230.0646-0.04790.3603-0.0879-0.0466-0.1512-0.78120.0616-0.01810.933-0.0208-0.27020.02340.01030.188655.62719.98235.305
40.8982-0.1291-0.58981.46091.53654.12660.00540.12350.0382-0.1467-0.1568-0.2374-0.45890.25910.15141.0604-0.0105-0.16330.14990.08550.162156.477-57.53423.837
52.6279-0.1074-0.13222.26261.4782.72980.00230.1272-0.47320.2062-0.0622-0.05780.81640.05530.05981.0861-0.0183-0.1140.01940.0060.175355.013-85.41738.991
61.51380.1913-0.80121.9519-0.72944.3303-0.1618-0.1165-0.00470.1438-0.098-0.2255-0.1010.78020.25990.7201-0.058-0.27570.20530.06020.176565.113-59.48554.313
71.7960.0311-0.08671.01860.00222.88130.1120.15550.132-0.3877-0.26930.2128-0.6483-1.24640.15731.05450.3379-0.38190.6228-0.10010.18830.56411.99913.335
81.2349-0.1151-0.70081.27440.43114.3362-0.3518-0.4568-0.2992-0.0024-0.0519-0.2631.28491.02110.40370.99550.3312-0.09010.33980.21070.295472.13-21.31926.946
92.2535-1.0951-0.64211.7120.43943.3024-0.16910.5541-0.1429-0.2589-0.43540.18851.0039-0.74060.60461.1252-0.1845-0.14670.3086-0.17960.269436.788-19.71614.341
100.1854-0.373-0.18311.68750.29032.5734-0.1104-0.12920.05030.5064-0.03970.01330.13430.31570.15011.1241-0.0311-0.25750.198-0.05180.119150.4983.06162.476
111.39850.23440.64372.18861.09763.33960.07020.0633-0.13170.2196-0.39720.450.2287-1.28240.3270.7224-0.1556-0.1240.8007-0.28890.312122.343-5.36939.422
121.14721.3033-1.25394.26970.48564.07040.1322-0.0869-0.0422-0.3734-0.0283-0.489-1.37180.7108-0.10391.3395-0.3322-0.20950.24290.04160.142464.08426.02122.102
131.38750.7279-0.06531.27490.33782.6680.0198-0.31760.13830.0787-0.33130.3042-0.7882-0.67930.31151.26310.1955-0.17770.2725-0.16630.203133.648-45.60257.063
140.69410.3750.35142.04460.33632.691-0.06490.119-0.2108-0.5765-0.0569-0.0908-0.44750.30840.12170.91510.0504-0.11450.1099-0.05780.128753.956-68.48511.36
151.847-0.4918-1.29772.07080.65843.17130.12270.30310.1042-0.2457-0.33190.3907-0.3698-1.33880.20920.77660.2004-0.32860.7481-0.20610.285322.813-59.87830.195
160.96620.8147-0.86043.219-1.08754.015-0.0235-0.2534-0.20810.5164-0.0867-0.12830.93640.61170.11021.09350.1976-0.08020.12890.05870.135661.466-91.51153.255
171.23060.23070.10931.5538-0.01662.18370.0052-0.1283-0.18530.2228-0.22920.29190.4773-1.03640.2241.1119-0.2125-0.07860.5334-0.13870.259227.131-77.27957.226
180.8733-0.1842-0.29721.3424-0.12153.8967-0.1540.12340.19510.17270.001-0.1479-1.22810.82920.15310.8715-0.3271-0.29780.22730.10010.219370.494-44.29249.563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 49
2X-RAY DIFFRACTION1A286 - 375
3X-RAY DIFFRACTION2B28 - 49
4X-RAY DIFFRACTION2B286 - 375
5X-RAY DIFFRACTION3C28 - 49
6X-RAY DIFFRACTION3C286 - 375
7X-RAY DIFFRACTION4D28 - 49
8X-RAY DIFFRACTION4D286 - 375
9X-RAY DIFFRACTION5E28 - 49
10X-RAY DIFFRACTION5E286 - 375
11X-RAY DIFFRACTION6F28 - 49
12X-RAY DIFFRACTION6F286 - 375
13X-RAY DIFFRACTION7A50 - 285
14X-RAY DIFFRACTION8A376 - 465
15X-RAY DIFFRACTION9B50 - 285
16X-RAY DIFFRACTION10B376 - 465
17X-RAY DIFFRACTION11C50 - 285
18X-RAY DIFFRACTION12C376 - 465
19X-RAY DIFFRACTION13D50 - 285
20X-RAY DIFFRACTION14D376 - 465
21X-RAY DIFFRACTION15E50 - 285
22X-RAY DIFFRACTION16E376 - 465
23X-RAY DIFFRACTION17F50 - 285
24X-RAY DIFFRACTION18F376 - 465

+
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://pdbjlvh1.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