[English] 日本語
Yorodumi
- PDB-3csy: Crystal structure of the trimeric prefusion Ebola virus glycoprot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3csy
TitleCrystal structure of the trimeric prefusion Ebola virus glycoprotein in complex with a neutralizing antibody from a human survivor
Components
  • (Envelope glycoprotein ...) x 2
  • Fab KZ52 heavy chain
  • Fab KZ52 light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / glycoprotein-antibody complex / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Ebola virus - Mayinga
Zaire (virus)
1976
MethodX-RAY DIFFRACTION / SYNCHROTRON / phase combination of model phases from an independently solved Fab KZ52, Fab KZ52 selenium anomalous signal / molecular replacement / Resolution: 3.4 Å
AuthorsLee, J.E. / Fusco, M.L. / Hessell, A.J. / Oswald, W.B. / Burton, D.R. / Saphire, E.O.
CitationJournal: Nature / Year: 2008
Title: Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor.
Authors: Lee, J.E. / Fusco, M.L. / Hessell, A.J. / Oswald, W.B. / Burton, D.R. / Saphire, E.O.
History
DepositionApr 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 2.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab KZ52 heavy chain
B: Fab KZ52 light chain
C: Fab KZ52 heavy chain
D: Fab KZ52 light chain
E: Fab KZ52 heavy chain
F: Fab KZ52 light chain
G: Fab KZ52 heavy chain
H: Fab KZ52 light chain
I: Envelope glycoprotein GP1
J: Envelope glycoprotein GP2
K: Envelope glycoprotein GP1
L: Envelope glycoprotein GP2
M: Envelope glycoprotein GP1
N: Envelope glycoprotein GP2
O: Envelope glycoprotein GP1
P: Envelope glycoprotein GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,07124
Polymers399,83716
Non-polymers6,2348
Water00
1
A: Fab KZ52 heavy chain
B: Fab KZ52 light chain
C: Fab KZ52 heavy chain
D: Fab KZ52 light chain
E: Fab KZ52 heavy chain
F: Fab KZ52 light chain
I: Envelope glycoprotein GP1
J: Envelope glycoprotein GP2
K: Envelope glycoprotein GP1
L: Envelope glycoprotein GP2
M: Envelope glycoprotein GP1
N: Envelope glycoprotein GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,41118
Polymers299,87812
Non-polymers4,5336
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45840 Å2
ΔGint-161 kcal/mol
Surface area97630 Å2
MethodPISA
2
G: Fab KZ52 heavy chain
H: Fab KZ52 light chain
O: Envelope glycoprotein GP1
P: Envelope glycoprotein GP2
hetero molecules

G: Fab KZ52 heavy chain
H: Fab KZ52 light chain
O: Envelope glycoprotein GP1
P: Envelope glycoprotein GP2
hetero molecules

G: Fab KZ52 heavy chain
H: Fab KZ52 light chain
O: Envelope glycoprotein GP1
P: Envelope glycoprotein GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,97918
Polymers299,87812
Non-polymers5,1026
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area46200 Å2
ΔGint-150 kcal/mol
Surface area96470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)273.710, 273.710, 409.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

-
Envelope glycoprotein ... , 2 types, 8 molecules IKMOJLNP

#3: Protein
Envelope glycoprotein GP1


Mass: 37027.480 Da / Num. of mol.: 4 / Fragment: deletion of residues 312-463 / Mutation: T42V, T230V
Source method: isolated from a genetically manipulated source
Details: Weak or discontinuous electron density is observed in the outer regions of the glycoprotein (residues 268-278 and 299-310) and these residues are tentatively assigned
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q05320
#4: Protein
Envelope glycoprotein GP2


Mass: 14779.716 Da / Num. of mol.: 4 / Fragment: deletion of residues 633-676
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P87666, UniProt: Q05320*PLUS

-
Antibody , 2 types, 8 molecules ACEGBDFH

#1: Antibody
Fab KZ52 heavy chain


Mass: 24208.557 Da / Num. of mol.: 4 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The antibody was identified from a human survivor of the 1995 Kikwit, Zaire Ebola virus outbreak
Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1
#2: Antibody
Fab KZ52 light chain


Mass: 23943.453 Da / Num. of mol.: 4 / Fragment: light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: The antibody was identified from a human survivor of the 1995 Kikwit, Zaire Ebola virus outbreak
Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-K1

-
Sugars , 4 types, 8 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8.5% (w/v) PEG 10,000, 0.1 M Tris-HCl pH 8.5, 0.4 M sodium acetate, 10% (v/v) PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9803 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2006
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9803 Å / Relative weight: 1
ReflectionResolution: 3.4→48.37 Å / Num. obs: 151305 / % possible obs: 96.2 % / Redundancy: 4.14 % / Rmerge(I) obs: 0.142 / Χ2: 0.94 / Net I/σ(I): 6.2 / Scaling rejects: 19362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
3.4-3.523.580.5681.754223148671.1494.7
3.52-3.663.640.507256023149431.1294.6
3.66-3.833.740.4582.357498148191.194.6
3.83-4.033.860.3892.759051148361.0894.2
4.03-4.283.930.2783.659880147701.0294
4.28-4.613.950.1974.761267150410.9495.6
4.61-5.084.230.157667624154120.9398
5.08-5.814.670.1456.775917157020.8899.8
5.81-7.324.780.1058.977102156620.899.6
7.32-48.374.90.04718.576813152530.6196.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
d*TREK9.6Ddata scaling
PHASERphasing
DMphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
BOSdata collection
d*TREKdata reduction
SHARPphasing
RefinementMethod to determine structure: phase combination of model phases from an independently solved Fab KZ52, Fab KZ52 selenium anomalous signal
Resolution: 3.4→48.369 Å / Cross valid method: THROUGHOUT / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.302 4405 3 %random
Rwork0.261 ---
obs0.263 146996 93.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.699 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 65.22 Å2 / Biso mean: 115.8 Å2 / Biso min: 240.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.338 Å2-0 Å20 Å2
2--1.338 Å20 Å2
3----2.677 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å / Luzzati sigma a obs: 0.97 Å
Refinement stepCycle: LAST / Resolution: 3.4→48.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23122 0 417 0 23539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01146668
X-RAY DIFFRACTIONf_angle_d1.183956
X-RAY DIFFRACTIONf_chiral_restr0.063760
X-RAY DIFFRACTIONf_plane_restr0.0057314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.4390.4561180.4074557467588
3.439-3.4790.3931290.3924533466289
3.479-3.5220.3831140.384507462190
3.522-3.5660.3571460.3744518466489
3.566-3.6130.3611410.3484592473390
3.613-3.6620.3741310.3524585471689
3.662-3.7150.3871510.3474588473991
3.715-3.770.3481460.3424496464290
3.77-3.8290.4271420.3344610475290
3.829-3.8920.3271590.3144580473990
3.892-3.9590.3161680.3044572474090
3.959-4.0310.321500.2974587473791
4.031-4.1080.331210.2844590471190
4.108-4.1920.2721620.2684669483192
4.192-4.2830.3161640.2624612477692
4.283-4.3830.3441530.2434697485093
4.383-4.4920.2831420.2294760490293
4.492-4.6140.231590.2234771493094
4.614-4.7490.2551420.2234854499695
4.749-4.9030.2621250.2174922504797
4.903-5.0780.2821650.2254996516198
5.078-5.2810.3011300.235005513599
5.281-5.5210.2821460.235055520199
5.521-5.8110.3111510.2315079523099
5.811-6.1750.3261620.2425018518099
6.175-6.650.2981640.2325034519899
6.65-7.3180.2911550.2295046520199
7.318-8.3720.2951450.1974974511998
8.372-10.530.1781790.1554964514398
10.53-48.3740.2771450.2424820496595
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)
1-0.01982.25150.97335.89080.99362.86490.02470.1147-0.16570.1984-0.20640.05660.223-0.09530.00010.6808-0.05620.02160.7412-0.03650.8338128.7742-96.2638-187.508
21.71610.0265-3.31883.1041-2.64854.30390.0697-0.3127-0.2029-0.0543-0.3588-0.19330.25780.331900.8940.0231-0.02540.910.05280.9332181.7777-120.2717-250.0211
33.7947-3.12821.02214.2746-0.50450.65540.14220.1603-0.16250.117-0.09220.16620.26410.071900.931-0.0414-0.09420.9944-0.06140.851396.9607-121.8991-262.471
41.80762.8751-0.26053.8174-1.97732.42650.03580.34050.0905-0.10560.0611-0.3254-0.0041-0.2704-00.85160.0386-0.09591.03270.01550.981389.9914-95.3477-280.9975
52.29441.3069-0.51851.3552.40092.83820.792-1.928-0.87691.1833-1.1964-0.61870.38020.0584-0.00011.5877-0.4572-0.12651.83340.38821.5702124.8446-94.8569-154.6656
60.9392-0.9444-1.53660.5621-0.2180.84790.24680.0415-0.6097-0.052-0.1814-0.49060.67310.4633-01.52930.2971-0.28981.3921-0.06621.7064211.3676-133.5396-258.5579
72.464-1.09240.8851.57090.10731.12720.2517-0.0894-0.61540.418-0.18640.22020.6004-0.351601.3961-0.2041-0.00031.2629-0.17381.17870.8993-136.6581-277.1601
81.35761.48530.38970.5279-1.877-0.48660.16660.4752-0.2237-0.69410.16910.38410.6555-0.88701.6464-0.112-0.36161.8340.07171.495559.3594-106.9302-289.9713
95.58610.4535-1.89982.33932.83324.66430.05680.0891-0.10980.4527-0.39210.84130.3002-0.910600.8795-0.23140.06681.0088-0.15871.1297109.9111-107.6098-185.0618
105.7775-0.98341.16861.4881.30753.9790.2802-0.91260.24510.0965-0.2958-0.51610.34490.7207-01.2359-0.0408-0.09011.24860.06721.0744189.7508-126.0151-230.1693
114.0801-0.22561.32980.91081.98154.59350.50870.6397-0.4618-0.2613-0.01860.02650.47020.3789-0.00011.10910.1608-0.10321.2785-0.14221.1779107.0689-138.6035-272.8723
124.6362-1.46440.27982.9466-0.58220.87820.22720.14340.7186-0.1480.08110.2372-0.3252-0.375-01.14230.05760.04521.12720.17841.185782.3722-78.3071-292.8916
130.3108-0.8568-1.08821.0804-0.59322.16330.6518-1.38920.47110.7806-0.84560.2718-0.1677-0.4722-0.00011.4992-0.41720.24482.0592-0.38431.8116109.5918-91.2436-151.8155
141.37990.09950.80721.9639-0.177-0.01050.34940.4605-0.0580.342-0.0707-0.1706-0.03150.1729-01.30460.1461-0.10221.79050.11471.5524221.7505-126.419-248.6445
151.96721.12411.23173.6914-0.3031.94930.00090.6779-0.30010.0693-0.1917-0.05640.45090.38080.00011.15360.1007-0.14971.6185-0.25841.015774.8678-139.7705-292.2048
160.40741.57420.99671.28710.77430.67640.6306-0.71020.219-0.15060.18771.50510.4848-0.74930.00031.51130.0176-0.00441.91480.60682.218848.968-95.2205-287.4831
17-0.07480.3028-0.22051.07370.50130.29390.37340.5281-1.0332-0.65120.35870.2508-0.37850.0731-00.97780.0841-0.19350.8564-0.01310.901130.4378-118.1736-201.4759
187.5785-7.403-6.59768.81534.64213.22070.7346-2.57964.0332-0.09221.7092-1.2007-1.46190.17890.27731.39480.1875-0.07481.3621-0.0071.239157.6645-129.0919-212.831
190.53920.2485-0.356-0.69632.2316-1.2701-0.3252-0.15980.10210.525-0.0695-0.15840.61890.01430.0011.15110.0095-0.17120.8942-0.00481.2322146.1736-126.0971-204.6469
204.18510.27550.3078-0.249-0.3223-0.2227-0.6386-3.09113.39911.1205-1.04810.34840.4256-0.166-0.09320.760.14870.14530.81540.18350.526126.8402-115.3571-204.9236
210.0884-0.1839-0.13281.3069-0.36270.6601-0.45640.7745-0.6269-0.39340.49370.05040.46870.1713-0.00010.929-0.047-0.12470.9125-0.02340.8935125.1622-129.5889-219.3034
220.4842-0.0192-0.39050.27840.33090.7134-0.1644-0.98990.6585-0.63291.51421.361-0.475-2.114-0.00061.2584-0.08240.13731.00550.08590.9937130.1069-115.4077-228.9853
231.97940.16120.21241.5359-0.886-0.5716-0.4763-0.2575-0.23520.11560.12770.3550.39810.1221-0.00021.0401-0.0488-0.03911.01850.1160.865112.8523-133.1564-243.0679
243.1847-0.88027.15811.7266-2.58321.9943-1.29770.3001-0.3098-0.5987-0.5735-0.6306-3.6973-3.868-0.16391.2237-0.16410.08691.45430.05020.9969112.2417-128.8076-212.9041
25-0.2097-0.1440.156-1.6218-0.40470.08980.92890.24880.49070.66820.10130.2664-0.26480.5027-0.00151.2226-0.07680.08391.23920.05841.2858110.0224-133.2785-227.9412
26-0.2124-0.07670.27510.2517-0.1040.01581.05192.74451.1286-0.5364-0.63470.62220.4012-2.00280.00110.9551-0.2491-0.06241.1729-0.33110.754117.1526-130.8705-248.8089
270.90280.1539-0.30430.3918-0.47190.03450.0496-0.8348-0.1777-0.07890.2853-0.88670.58670.20650.00020.9198-0.1150.06191.0563-0.16231.0937133.6-136.7435-238.2139
280.19680.05990.2430.19620.09740.44410.03881.8305-0.4222-1.7704-0.7944-0.0822-1.169-0.2722-0.00241.1085-0.0327-0.21141.0471-0.05990.943135.2544-119.5401-237.7493
290.990.047-0.08430.2452-2.63580.00630.1002-0.39790.11370.44750.02290.04530.9361-0.15560.00030.9677-0.0774-0.01340.8388-0.16490.9961161.7005-132.3847-237.2762
30-0.25190.04030.08660.23010.09050.0421.25041.94142.5061-0.04441.8836-0.53281.22011.8926-0.0011.5377-0.0004-0.04851.1877-0.21521.0071134.8696-143.0281-250.9134
310.34030.31410.1205-0.5737-1.3613-0.20820.4059-0.3071-1.0449-0.9534-0.7328-0.5048-0.5867-0.26690.00051.3476-0.05330.17040.8875-0.2851.0819149.447-141.0693-245.2065
32-0.02120.03710.29550.133-0.1864-0.11640.1560.2477-0.5655-0.56570.66-0.098-1.29013.27540.00310.7555-0.0116-0.18330.8876-0.1540.8068162.5825-127.1227-233.9961
330.4101-0.016-1.7371.12850.37040.89050.2296-0.8063-0.30730.5144-0.46250.45150.2688-0.80880.00061.04950.1068-0.05570.7995-0.11990.6734146.8818-131.142-221.6408
340.4784-0.00830.17380.30260.07760.20260.7007-0.07740.3111.3976-1.0513-1.3747-1.6317-0.11310.00061.1463-0.0595-0.02821.2741-0.19060.8355141.4699-116.2302-229.006
350.0833-0.10610.0518-0.3373-0.5115-0.24220.39070.333-0.2154-1.04060.0497-0.15530.29830.2673-0.00040.90670.18170.00021.2683-0.22031.3108109.7196-88.5157-297.5957
36-0.0524-0.148-0.08250.06180.03640.2089-1.6682-2.2399-1.2480.4073-0.11411.26091.98970.9308-0.00121.4955-0.1463-0.17221.1695-0.05291.1486136.3162-105.9772-303.685
370.7164-0.78860.3107-0.1607-1.16-0.1229-0.15911.07710.03110.0113-0.07130.41810.2544-0.56780.0011.2076-0.13370.06710.8812-0.07851.3061121.7145-99.2598-302.8852
380.0789-0.4436-0.01190.27730.38440.1117-0.4190.67-1.32482.5630.47963.3109-0.0749-0.9837-0.00240.75620.1429-0.0860.9246-0.21971.0772109.491-83.4144-293.3346
390.070.7237-0.14620.6050.40470.3607-0.08680.8613-0.14130.1043-0.6195-0.1110.29340.328301.1158-0.0369-0.01550.7533-0.0551.0633125.345-73.6442-301.8608
400.1482-0.19310.3625-0.1213-0.00890.3101-0.2934-1.85230.31040.41720.51372.4888-1.611-0.38080.00010.8777-0.1754-0.06461.12060.04581.2645131.3-75.8731-285.4859
413.0588-1.17470.25762.45461.06941.91650.05680.48280.1082-0.27020.3495-0.2016-0.28710.0805-0.00020.8425-0.0018-0.11480.7937-0.07390.8369128.1302-120.0333-209.5926
421.52060.1561-0.66511.6583-0.71394.8983-0.1469-0.3169-0.59210.1036-0.0076-0.37130.5589-0.10670.00010.9299-0.0495-0.02840.80120.08990.963128.6212-137.8083-204.0036
431.81320.0195-2.08121.25830.10731.6576-0.0744-0.4849-0.7832-0.07340.2546-0.010.37820.1019-0.00021.24520.0461-0.00921.02650.19160.993129.8622-142.3969-181.8504
440.82630.33290.52020.2385-0.57941.27561.2091-0.3099-0.1490.8367-2.2747-1.48470.5685-0.1063-0.00211.2962-0.0661-0.01530.5547-0.09991.0387126.1694-146.2603-174.9323
451.7435-0.4635-0.21931.07090.96333.4793-0.3756-0.07920.4586-0.4680.53540.0419-0.32210.1510.00020.8601-0.0819-0.14421.2287-0.00030.8658121.612-132.1937-243.8674
462.77831.31410.59413.5576-0.43751.5590.0849-0.0338-0.60530.3217-0.22930.28160.4927-0.4046-0.00011.194-0.1551-0.03580.9476-0.09410.9243121.0592-149.2132-236.2021
470.87470.19920.23530.27360.81280.2007-0.253-0.5396-0.70230.7846-0.1272-0.11420.2919-0.79340.00031.5143-0.3926-0.22791.4444-0.09761.6521102.986-162.5207-239.7395
480.4354-0.1505-0.2551-0.2010.05940.3393-0.413-0.226-0.83151.1655-0.341.00120.14010.047-0.00121.599-0.0128-0.40481.28510.1811.5072100.5819-171.2033-242.1005
493.62451.9132-0.4570.2324-0.04872.0406-0.02130.31680.89630.39030.0232-0.3057-0.4183-0.34750.00011.0692-0.0715-0.05580.8669-0.15290.8472156.5489-129.0055-231.4226
503.1287-0.1052-0.45863.0189-0.24071.50680.04050.0964-0.3783-0.05030.0509-0.06860.60780.006-0.00011.09240.0617-0.07580.7918-0.07940.951154.8026-146.5762-225.5654
511.4577-0.37420.50841.0121-1.3431.0992-0.21770.1072-0.2624-0.12430.5582-0.52860.57340.0044-0.00021.37710.10670.14260.9585-0.18691.3062170.4866-161.9418-231.3648
520.2519-0.9336-0.01710.256-0.0390.4627-1.05390.72890.3535-0.86391.09630.84951.42730.42080.00151.1825-0.23610.20160.92650.06631.1473176.2528-168.2916-228.1748
533.0215-1.7434-1.19961.5724-0.04760.0738-0.0983-0.4504-0.17820.1420.0621-0.2683-0.2927-0.1786-0.00010.9992-0.12040.04230.8946-0.07341.1904115.514-81.841-296.1242
542.21320.290.21181.5357-0.20212.667-0.04550.48350.2058-0.75780.20450.23970.211-0.171101.0872-0.0235-0.17951.2173-0.00451.1163116.6417-82.5362-314.8001
551.5644-0.31290.2223-0.2530.10790.74050.10890.6325-1.2323-0.85960.0825-0.3829-0.27890.010701.4236-0.016-0.21371.78780.09861.5275100.3207-93.024-326.7007
560.06140.0346-0.1506-0.1791-0.1055-0.0607-0.1149-0.35811.7057-1.22890.74450.72561.1152-1.06150.00190.848-0.00720.07652.16360.17291.214892.084-89.6662-331.4657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2C1 - 119
3X-RAY DIFFRACTION3E1 - 119
4X-RAY DIFFRACTION4G1 - 119
5X-RAY DIFFRACTION5A120 - 228
6X-RAY DIFFRACTION6C120 - 228
7X-RAY DIFFRACTION7E120 - 228
8X-RAY DIFFRACTION8G120 - 228
9X-RAY DIFFRACTION9B1 - 111
10X-RAY DIFFRACTION10D1 - 111
11X-RAY DIFFRACTION11F1 - 111
12X-RAY DIFFRACTION12H1 - 111
13X-RAY DIFFRACTION13B112 - 211
14X-RAY DIFFRACTION14D112 - 211
15X-RAY DIFFRACTION15F112 - 211
16X-RAY DIFFRACTION16H112 - 211
17X-RAY DIFFRACTION17J502 - 520
18X-RAY DIFFRACTION18J523 - 533
19X-RAY DIFFRACTION19J534 - 551
20X-RAY DIFFRACTION20J552 - 564
21X-RAY DIFFRACTION21J565 - 585
22X-RAY DIFFRACTION22J586 - 599
23X-RAY DIFFRACTION23L503 - 522
24X-RAY DIFFRACTION24L525 - 533
25X-RAY DIFFRACTION25L534 - 551
26X-RAY DIFFRACTION26L552 - 564
27X-RAY DIFFRACTION27L565 - 585
28X-RAY DIFFRACTION28L586 - 597
29X-RAY DIFFRACTION29N502 - 521
30X-RAY DIFFRACTION30N524 - 533
31X-RAY DIFFRACTION31N534 - 551
32X-RAY DIFFRACTION32N552 - 564
33X-RAY DIFFRACTION33N565 - 585
34X-RAY DIFFRACTION34N586 - 599
35X-RAY DIFFRACTION35P503 - 521
36X-RAY DIFFRACTION36P525 - 533
37X-RAY DIFFRACTION37P534 - 551
38X-RAY DIFFRACTION38P552 - 564
39X-RAY DIFFRACTION39P565 - 585
40X-RAY DIFFRACTION40P586 - 599
41X-RAY DIFFRACTION41I31 - 88
42X-RAY DIFFRACTION42I89 - 230
43X-RAY DIFFRACTION43I231 - 265
44X-RAY DIFFRACTION44I266 - 310
45X-RAY DIFFRACTION45K31 - 88
46X-RAY DIFFRACTION46K89 - 230
47X-RAY DIFFRACTION47K231 - 265
48X-RAY DIFFRACTION48K266 - 309
49X-RAY DIFFRACTION49M31 - 88
50X-RAY DIFFRACTION50M89 - 230
51X-RAY DIFFRACTION51M231 - 265
52X-RAY DIFFRACTION52M266 - 308
53X-RAY DIFFRACTION53O31 - 88
54X-RAY DIFFRACTION54O89 - 230
55X-RAY DIFFRACTION55O231 - 266
56X-RAY DIFFRACTION56O273 - 308

+
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