[English] 日本語
Yorodumi
- PDB-7dpm: Crystal structure of SARS-CoV-2 Spike RBD in complex with MW06 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dpm
TitleCrystal structure of SARS-CoV-2 Spike RBD in complex with MW06 Fab
Components
  • Spike protein S1
  • heavy chain of MW06
  • light chain of MW06
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV-2 / Spike / RBD / Antibody / ADE / VIRUS / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.304 Å
AuthorsWang, J. / Jiao, S. / Wang, R. / Zhang, J. / Zhang, M. / Wang, M.
CitationJournal: Mabs / Year: 2021
Title: Characterization of MW06, a human monoclonal antibody with cross-neutralization activity against both SARS-CoV-2 and SARS-CoV.
Authors: Jiang, W. / Wang, J. / Jiao, S. / Gu, C. / Xu, W. / Chen, B. / Wang, R. / Chen, H. / Xie, Y. / Wang, A. / Li, G. / Zeng, D. / Zhang, J. / Zhang, M. / Wang, S. / Wang, M. / Gui, X.
History
DepositionDec 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: heavy chain of MW06
B: light chain of MW06
C: Spike protein S1
D: heavy chain of MW06
E: light chain of MW06
F: Spike protein S1
G: heavy chain of MW06
H: light chain of MW06
I: Spike protein S1
J: heavy chain of MW06
K: light chain of MW06
L: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,04116
Polymers291,80612
Non-polymers1,2344
Water81145
1
A: heavy chain of MW06
B: light chain of MW06
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5224
Polymers72,9523
Non-polymers5711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: heavy chain of MW06
E: light chain of MW06
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1734
Polymers72,9523
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: heavy chain of MW06
H: light chain of MW06
I: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1734
Polymers72,9523
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: heavy chain of MW06
K: light chain of MW06
L: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1734
Polymers72,9523
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.130, 153.830, 172.690
Angle α, β, γ (deg.)90.000, 95.880, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 130 or resid 148 through 227))
21(chain D and (resid 1 through 130 or resid 148 through 227))
31(chain G and (resid 1 through 130 or resid 148 through 227))
41chain J
12(chain B and resid 1 through 212)
22(chain E and resid 1 through 212)
32(chain H and resid 1 through 212)
42chain K
13(chain C and resid 333 through 527)
23(chain F and resid 333 through 527)
33(chain I and resid 333 through 527)
43(chain L and resid 333 through 527)

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
111GLUGLUTHRTHR(chain A and (resid 1 through 130 or resid 148 through 227))AA1 - 1301 - 130
121GLYGLYPROPRO(chain A and (resid 1 through 130 or resid 148 through 227))AA148 - 227148 - 227
211GLUGLUTHRTHR(chain D and (resid 1 through 130 or resid 148 through 227))DD1 - 1301 - 130
221GLYGLYPROPRO(chain D and (resid 1 through 130 or resid 148 through 227))DD148 - 227148 - 227
311GLUGLUTHRTHR(chain G and (resid 1 through 130 or resid 148 through 227))GG1 - 1301 - 130
321GLYGLYPROPRO(chain G and (resid 1 through 130 or resid 148 through 227))GG148 - 227148 - 227
411GLUGLUPROPROchain JJJ1 - 2271 - 227
112ASPASPGLYGLY(chain B and resid 1 through 212)BB1 - 2121 - 212
212ASPASPGLYGLY(chain E and resid 1 through 212)EE1 - 2121 - 212
312ASPASPGLYGLY(chain H and resid 1 through 212)HH1 - 2121 - 212
412ASPASPGLYGLYchain KKK1 - 2121 - 212
113THRTHRPROPRO(chain C and resid 333 through 527)CC333 - 52715 - 209
213THRTHRPROPRO(chain F and resid 333 through 527)FF333 - 52715 - 209
313THRTHRPROPRO(chain I and resid 333 through 527)II333 - 52715 - 209
413THRTHRPROPRO(chain L and resid 333 through 527)LL333 - 52715 - 209

NCS ensembles :
ID
1
2
3

-
Components

-
Antibody , 2 types, 8 molecules ADGJBEHK

#1: Antibody
heavy chain of MW06


Mass: 24390.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
light chain of MW06


Mass: 23439.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Protein / Non-polymers , 2 types, 49 molecules CFIL

#3: Protein
Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 25122.336 Da / Num. of mol.: 4 / Fragment: RBD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 2 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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.: 3 / 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

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 12% EG, 0.1 M Citrate-Na, pH 3.5, 14% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 57134 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.069 / Rrim(I) all: 0.18 / Χ2: 0.981 / Net I/σ(I): 4.7 / Num. measured all: 390068
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.426.41.21157140.6520.5181.3190.967100
3.42-3.556.70.88756890.7750.3710.9630.979100
3.55-3.727.10.65856600.8820.2650.710.991100
3.72-3.917.10.44457290.940.1790.4790.992100
3.91-4.1670.28256660.9740.1150.3050.987100
4.16-4.486.60.17656970.9860.0740.1910.971100
4.48-4.936.90.14357160.990.0580.1540.976100
4.93-5.647.10.12857370.990.0520.1380.976100
5.64-7.16.60.10957260.9910.0460.1190.98599.9
7.1-506.70.07858000.9950.0330.0850.9899.6

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG, 6JJP

6lzg

6jjp


Resolution: 3.304→47.52 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 2795 4.91 %
Rwork0.2174 54152 -
obs0.2197 56947 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.28 Å2 / Biso mean: 95.113 Å2 / Biso min: 30.38 Å2
Refinement stepCycle: final / Resolution: 3.304→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19446 0 80 45 19571
Biso mean--103.96 51.5 -
Num. residues----2531
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3819X-RAY DIFFRACTION9.892TORSIONAL
12D3819X-RAY DIFFRACTION9.892TORSIONAL
13G3819X-RAY DIFFRACTION9.892TORSIONAL
14J3819X-RAY DIFFRACTION9.892TORSIONAL
21B4063X-RAY DIFFRACTION9.892TORSIONAL
22E4063X-RAY DIFFRACTION9.892TORSIONAL
23H4063X-RAY DIFFRACTION9.892TORSIONAL
24K4063X-RAY DIFFRACTION9.892TORSIONAL
31C3727X-RAY DIFFRACTION9.892TORSIONAL
32F3727X-RAY DIFFRACTION9.892TORSIONAL
33I3727X-RAY DIFFRACTION9.892TORSIONAL
34L3727X-RAY DIFFRACTION9.892TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.304-3.36060.34881570.349248992
3.3606-3.42170.39761420.32472745100
3.4217-3.48750.35031440.30922673100
3.4875-3.55870.3351490.29512709100
3.5587-3.6360.30361540.28032692100
3.636-3.72060.32931650.26872690100
3.7206-3.81360.3281460.2682703100
3.8136-3.91670.31891190.24892754100
3.9167-4.03190.2571290.23632710100
4.0319-4.16190.29581340.21932722100
4.1619-4.31060.23341180.20712764100
4.3106-4.4830.23991350.18042716100
4.483-4.68690.20321100.17642733100
4.6869-4.93380.22551420.18382730100
4.9338-5.24250.21321380.17492731100
5.2425-5.64670.21331530.1842719100
5.6467-6.21380.26041500.1952707100
6.2138-7.11040.24331590.197270399
7.1104-8.94860.25141200.1966275699
8.9486-47.520.24061310.1998270697

+
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