[English] 日本語
Yorodumi
- PDB-6vw1: Structure of SARS-CoV-2 chimeric receptor-binding domain complexe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vw1
TitleStructure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2
Components
  • Angiotensin-converting enzyme 2
  • SARS-CoV-2 chimeric RBD
KeywordsCELL INVASION / coronavirus
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / Attachment and Entry / negative regulation of signaling receptor activity / carboxypeptidase activity / regulation of cytokine production / positive regulation of cardiac muscle contraction / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / cilium / endocytosis involved in viral entry into host cell / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / SARS-CoV-1 activates/modulates innate immune responses / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / endopeptidase activity / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / Potential therapeutics for SARS / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont entry into host cell / membrane raft / apical plasma membrane / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human SARS coronavirus
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsShang, J. / Ye, G. / Shi, K. / Wan, Y.S. / Aihara, H. / Li, F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI089728 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI089728 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Nature / Year: 2020
Title: Structural basis of receptor recognition by SARS-CoV-2.
Authors: Shang, J. / Ye, G. / Shi, K. / Wan, Y. / Luo, C. / Aihara, H. / Geng, Q. / Auerbach, A. / Li, F.
History
DepositionFeb 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Apr 8, 2020Group: Database references / Structure summary / Category: audit_author / citation
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Apr 15, 2020Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
Revision 1.4May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_ec
Revision 1.5May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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
A: Angiotensin-converting enzyme 2
B: Angiotensin-converting enzyme 2
E: SARS-CoV-2 chimeric RBD
F: SARS-CoV-2 chimeric RBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,75124
Polymers186,9664
Non-polymers5,78520
Water46826
1
A: Angiotensin-converting enzyme 2
E: SARS-CoV-2 chimeric RBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,47611
Polymers93,4832
Non-polymers2,9939
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme 2
F: SARS-CoV-2 chimeric RBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,27613
Polymers93,4832
Non-polymers2,79211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.435, 118.034, 112.075
Angle α, β, γ (deg.)90.000, 93.120, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERTYRTYR(chain 'A' and resid 19 through 614)AA19 - 6131 - 595
211SERSERTYRTYR(chain 'B' and resid 19 through 614)BB19 - 6131 - 595
112THRTHRSERSER(chain 'E' and (resid 376 through 384 or resid 386...EC376 - 38358 - 65
122LYSLYSLYSLYS(chain 'E' and (resid 376 through 384 or resid 386...EC38668
132ASPASPILEILE(chain 'E' and (resid 376 through 384 or resid 386...EC389 - 44171 - 123
142THRTHRTHRTHR(chain 'E' and (resid 376 through 384 or resid 386...EC444126
152ASNASNASNASN(chain 'E' and (resid 376 through 384 or resid 386...EC448130
162ASNASNPHEPHE(chain 'E' and (resid 376 through 384 or resid 386...EC450 - 456132 - 138
172ARGARGASPASP(chain 'E' and (resid 376 through 384 or resid 386...EC466 - 467148 - 149
182GLNGLNGLNGLN(chain 'E' and (resid 376 through 384 or resid 386...EC474156
192THRTHRTHRTHR(chain 'E' and (resid 376 through 384 or resid 386...EC478160
1102GLYGLYVALVAL(chain 'E' and (resid 376 through 384 or resid 386...EC482 - 483164 - 165
1112PROPROASNASN(chain 'E' and (resid 376 through 384 or resid 386...EC491 - 501173 - 183
212THRTHRSERSER(chain 'F' and (resid 376 through 384 or resid 386...FD376 - 38358 - 65
222LYSLYSLYSLYS(chain 'F' and (resid 376 through 384 or resid 386...FD38668
232ASPASPILEILE(chain 'F' and (resid 376 through 384 or resid 386...FD389 - 44171 - 123
242THRTHRTHRTHR(chain 'F' and (resid 376 through 384 or resid 386...FD444126
252ASNASNASNASN(chain 'F' and (resid 376 through 384 or resid 386...FD448130
262ASNASNPHEPHE(chain 'F' and (resid 376 through 384 or resid 386...FD450 - 456132 - 138
272ARGARGASPASP(chain 'F' and (resid 376 through 384 or resid 386...FD466 - 467148 - 149
282GLNGLNGLNGLN(chain 'F' and (resid 376 through 384 or resid 386...FD474156
292THRTHRTHRTHR(chain 'F' and (resid 376 through 384 or resid 386...FD478160
2102GLYGLYVALVAL(chain 'F' and (resid 376 through 384 or resid 386...FD482 - 483164 - 165
2112PROPROASNASN(chain 'F' and (resid 376 through 384 or resid 386...FD491 - 501173 - 183

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ABEF

#1: Protein Angiotensin-converting enzyme 2 / / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15


Mass: 69153.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein SARS-CoV-2 chimeric RBD / S glycoprotein / E2 / Peplomer protein


Mass: 24329.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human SARS coronavirus, (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59594, UniProt: P0DTC2

-
Sugars , 4 types, 12 molecules

#3: 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 natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 5 / Source method: isolated from a natural source
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
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 789.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-1/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#9: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

-
Non-polymers , 4 types, 34 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cl
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris, PEG 6000, and 100 mM NaCl.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.68→118.03 Å / Num. obs: 58219 / % possible obs: 96.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 85.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.08
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 4 % / Rmerge(I) obs: 1.47 / Num. unique obs: 5774 / CC1/2: 0.587 / % possible all: 98.97

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJF

2ajf


Resolution: 2.68→59.02 Å / SU ML: 0.4455 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1336
RfactorNum. reflection% reflection
Rfree0.2288 2674 4.6 %
Rwork0.197 --
obs0.1985 58159 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 108.85 Å2
Refinement stepCycle: LAST / Resolution: 2.68→59.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12782 0 372 26 13180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002613506
X-RAY DIFFRACTIONf_angle_d0.59718350
X-RAY DIFFRACTIONf_chiral_restr0.04392001
X-RAY DIFFRACTIONf_plane_restr0.0042339
X-RAY DIFFRACTIONf_dihedral_angle_d21.18174914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.730.40551580.38162849X-RAY DIFFRACTION99.11
2.73-2.780.39821300.35222938X-RAY DIFFRACTION98.84
2.78-2.840.36111640.33552878X-RAY DIFFRACTION99.25
2.84-2.90.35841490.31332901X-RAY DIFFRACTION99.12
2.9-2.970.33681450.30052929X-RAY DIFFRACTION99.1
2.97-3.040.31911400.29632832X-RAY DIFFRACTION96.62
3.04-3.120.34781410.28472893X-RAY DIFFRACTION98.35
3.12-3.220.35041380.27552908X-RAY DIFFRACTION98.99
3.22-3.320.3321360.26912933X-RAY DIFFRACTION99.38
3.32-3.440.29591080.24552944X-RAY DIFFRACTION99.38
3.44-3.580.25581340.22212936X-RAY DIFFRACTION99.22
3.58-3.740.25671290.22452941X-RAY DIFFRACTION99.19
3.74-3.940.22171440.19482917X-RAY DIFFRACTION99.32
3.94-4.180.22591380.17922932X-RAY DIFFRACTION99.16
4.18-4.50.18941280.16232913X-RAY DIFFRACTION97.75
4.5-4.960.17781840.15442899X-RAY DIFFRACTION99.61
4.96-5.670.19771270.16462957X-RAY DIFFRACTION99.71
5.67-7.150.20921410.18432992X-RAY DIFFRACTION99.71
7.15-59.020.18271400.15642993X-RAY DIFFRACTION98.71
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)
15.326795728621.31941146559-0.8631084933574.846094717540.1829330816215.69493657444-0.1346049461840.222295960087-0.2538730681860.301929156454-0.142808577383-0.4448679404510.543275180320.0001902588519330.2717192476370.743662271292-0.181875017609-0.02368548161150.6691052701980.1134056041140.7642793941990.516405952-16.0765706333175.880993265
24.436458281921.89409022778-1.86319593911.89553681299-1.323791938672.29207082879-0.1603072998280.255933361835-0.114950033341-0.1235138530540.0741039290462-0.08819637649430.416007534023-0.2151180999930.1282378574690.7807807438330.08294147744240.09463381095640.5981186004520.0356924286040.700900070338110.12787697-3.84500303203157.093174917
33.372430885811.65172975031-2.27949095655.21186781177-2.146181527534.49057632831.007095311060.2214605557651.740911462850.718952758963-0.1863550155740.350815759827-1.02571803811-0.348788092541-0.7117772022470.860189355873-0.001219271608090.2840045304840.6886642566180.1516893359651.3367533546693.809316578110.5700401803169.216991716
44.043060861892.0298966626-1.661550264251.62321555429-0.6962806122543.147748486810.06470742746290.7172323730780.672780574358-0.3073241184920.2753665364060.1792617086550.175372653853-0.634291615699-0.2539452550980.6676234249890.04013038176930.07497636333090.6208676380370.2407282192320.772820083301104.503541991.71528205753152.360249837
57.568510849112.97571139846-4.199264216162.38487702852-1.65933599992.34448862109-0.1809618721331.869969957841.38279582952-0.3894093036710.7870677987820.6020833465860.137055209552-0.95993294913-0.6112955227220.865267382804-0.03276035835720.01213969055231.188062739170.4204583268480.917198796774102.7393908536.6159986961143.880093958
62.625802172550.386314152748-0.5727152567742.58278301757-1.290460107532.85472984472-0.3425314266350.703811478449-0.163734822151-0.6145286874340.6009818329870.2244840445390.360598020045-0.594297580669-0.2399913543781.10535235154-0.244826640988-0.03636877832261.26589205990.09638840192120.60645574750373.245556587438.447092426895.5594578639
73.278937314950.838664221298-0.490151675414.61345077428-1.79212608152.571253017020.005525524797090.5836321642510.6969320427270.1008602631440.7488782673851.13078979347-0.667490316907-1.35021817294-0.6373441784310.864107615749-0.02638184115340.03041758792391.292257476450.5442153270171.1265286410648.976455010737.5759850018116.490504588
83.040009626840.741321687564-1.073024292773.56398555175-0.6770011194775.09110348811-0.2380357901480.459558985221-0.228908182647-0.3511440403110.5504345821630.240630536622-0.100174342389-0.478056851035-0.2949191150840.685456335685-0.143268353728-0.0001626489351070.6859517687390.09270857033760.67930365371160.322534171220.403118499120.868545144
92.52909456907-0.976521965945-1.719060691424.58127366705-0.3825661370316.50123854237-0.2051881134510.2570272961460.111673451609-0.2827283768870.343704754260.169333628444-0.40161808187-0.522777866965-0.09129096780390.565199399555-0.059546870287-0.07687132614880.8227817210787.16291288097E-50.61397565081177.360925265840.9293255371123.046391634
103.887273469020.475848967388-1.247887760034.158991092120.7952384957977.92720025282-0.288691810538-0.0742833748106-0.158826993315-0.2296669828170.252742122691-0.2024031976670.4237772810330.3421094481790.09396535864090.449661474277-0.00737620405782-0.06781911481540.570277748072-0.0314607309430.63156712966978.81397175428.4576727618124.246093814
115.199875627080.90587668677-0.1663851906723.09335772745-1.232274913072.65267703626-0.3010633383260.780208333847-0.210974211164-0.6409203972460.5800916886340.1842054035050.404274527614-0.534982579778-0.2690049338460.714779707013-0.20420873849-0.03186741246050.7413079848790.01691218450560.50972109284765.982575671921.7754501214117.381504166
128.979096121621.19472956879-0.4095195323764.05771592124-3.427644968215.96645594226-0.380820294998-0.0164967321859-0.767229875263-0.2404349612720.4781883827550.04458727190060.353188740586-0.672934530821-0.1285796788530.806414012399-0.23283888240.09123355266340.678793333611-0.06154777537590.74033860995756.943627639113.2827563184130.988625902
136.30083715914-3.81295086689-0.4018496217978.34785198651-1.234919481923.649908513440.0349137960195-0.541718867315-0.1498627104970.6387865281340.07220884154820.791583276621-1.08848815265-1.102811151270.05184935553951.14872233691-0.1602127714810.1708466082911.34406032764-0.04470819838870.76818200865358.3056598764-3.69792593979194.993680431
142.09204065483-1.891748133543.776409094597.23974803737-2.253561585879.13784286684-0.6148721640780.5862443899552.44143738017-0.941422027602-0.065811533314-0.257564217495-0.243417254206-0.7418547700380.7007773914811.28049419352-0.0668056332508-0.1753757872451.341613631120.2327876924991.2180334919359.42032992325.97477374565184.755107742
158.08110724476-2.23485052574-1.087583249925.34916078064-0.2204298387192.900644332790.08863170501580.612889418538-0.146247078995-0.0940492886340.01336850718480.361231078536-0.132953064784-0.571074051491-0.0863413886220.839591381631-0.26784349994-0.02511749278020.971723394220.02218251991840.46524491917963.8315588115-8.78287962048183.118887646
169.71854270042-6.81611490361-4.179481628594.808041681582.548358536575.29568719452-0.3754487747250.330853232422-1.529068369060.294103979422-0.2259041942710.2367214014431.37792675947-0.4871466536990.5124310713061.21231114197-0.4368455209560.03599094676120.936919130379-0.1259689286180.95988963190474.7839286341-29.6121843415177.401376898
175.127247517-2.03582331462-0.7955500183553.36759738265-0.4631017968771.7896591573-0.1103397502530.835289717509-0.1148150679890.2865097420630.02177027232820.294661600691-0.535747001544-0.419810807960.09629125984050.96454823269-0.2443298837830.08228304616281.04692281419-0.05437344333750.69059853155963.0958551999-3.70621806686187.121884936
188.71189874394-1.392514861793.226739563952.608266716642.559493558825.3987908716-0.7876655736730.7499950033840.416809902037-0.4407282229910.384814242647-1.42763320754-0.6150038595910.9348401050770.3223901790931.09399494894-0.1470451431030.07264404915541.070052013950.2537818625741.59942981506112.53138802262.9388556829102.386907824
199.798213380482.254454366780.6035557158883.396882004612.407175239829.21106891722-0.3864819777010.1424749973310.8153504534720.145015610552-0.0877259040472-0.5667588888410.1693435155851.085911992080.3436961368230.9155360009610.009506549117230.08733221188830.8623003850210.2831292759651.36319607896112.80390016356.8892580386104.02593545
202.173217160642.204591166291.968937878423.289834912134.147344915226.19419907792-1.095999681511.02533346804-0.3020957783340.07083809243340.966595669568-0.8251600090740.1738497604142.34310503844-0.06875321007190.9623532765110.102927492179-0.02914612369871.720159860950.5010458277911.6449179467119.89140003149.4702352116107.830136363
214.39148689502-0.2948635573740.8384730532183.205073779850.6492949768195.76314108006-0.02306902537390.7756096932790.0834081181287-0.239901378713-0.322972796728-0.6555517188860.638316954055-0.03624807710010.2949030706940.8787309332250.04109200024430.2303081207730.7130609286020.1296256909210.872115641004101.35956626946.078223392395.0119461894
220.9243209805610.00969616644232-2.256156087521.83471236651-1.419823967436.383646330810.329827379040.5216964573960.553289136172-0.489621958272-0.162704470322-0.09015681505370.609685531259-1.08604631328-0.02293559743761.00212255961-0.03944760887320.08307468140081.14119848986-0.002047195657110.81242764208588.697406201945.486564657892.3667181071
232.18684089696-2.144971242992.390415798647.311268851132.481169457237.01487346695-0.2698713478971.07380067040.1858842826140.566839457243-0.312433744311-0.979877873684-0.1064634076491.658152992520.5741877521240.841813635570.02794123815970.0339877800671.167892792080.5909298476970.941352245609116.07730072254.201559252102.147282828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 293 )
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 431 )
4X-RAY DIFFRACTION4chain 'A' and (resid 432 through 560 )
5X-RAY DIFFRACTION5chain 'A' and (resid 561 through 614 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 193 )
8X-RAY DIFFRACTION8chain 'B' and (resid 194 through 293 )
9X-RAY DIFFRACTION9chain 'B' and (resid 294 through 384 )
10X-RAY DIFFRACTION10chain 'B' and (resid 385 through 431 )
11X-RAY DIFFRACTION11chain 'B' and (resid 432 through 581 )
12X-RAY DIFFRACTION12chain 'B' and (resid 582 through 614 )
13X-RAY DIFFRACTION13chain 'E' and (resid 334 through 369 )
14X-RAY DIFFRACTION14chain 'E' and (resid 370 through 385 )
15X-RAY DIFFRACTION15chain 'E' and (resid 386 through 469 )
16X-RAY DIFFRACTION16chain 'E' and (resid 470 through 494 )
17X-RAY DIFFRACTION17chain 'E' and (resid 495 through 527 )
18X-RAY DIFFRACTION18chain 'F' and (resid 331 through 349 )
19X-RAY DIFFRACTION19chain 'F' and (resid 350 through 374 )
20X-RAY DIFFRACTION20chain 'F' and (resid 375 through 394 )
21X-RAY DIFFRACTION21chain 'F' and (resid 395 through 479 )
22X-RAY DIFFRACTION22chain 'F' and (resid 480 through 506 )
23X-RAY DIFFRACTION23chain 'F' and (resid 507 through 527 )

+
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