[English] 日本語
Yorodumi
- PDB-7jmp: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jmp
TitleCrystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-39
Components
  • COVA2-39 heavy chain
  • COVA2-39 light chain
  • Spike protein S1
KeywordsViral Protein/IMMUNE SYSTEM / SARS-CoV-2 / COVID-19 / RBD / Antibody / SARS / Spike / IMMUNE SYSTEM / Viral Protein-IMMUNE SYSTEM 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / 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 / fusion of virus membrane with host plasma membrane / 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 / membrane / identical protein binding / 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 / 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 ...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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.712 Å
AuthorsWu, N.C. / Yuan, M. / Liu, H. / Zhu, X. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI139445 United States
Bill & Melinda Gates FoundationOPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657
CitationJournal: Cell Rep / Year: 2020
Title: An Alternative Binding Mode of IGHV3-53 Antibodies to the SARS-CoV-2 Receptor Binding Domain.
Authors: Wu, N.C. / Yuan, M. / Liu, H. / Lee, C.D. / Zhu, X. / Bangaru, S. / Torres, J.L. / Caniels, T.G. / Brouwer, P.J.M. / van Gils, M.J. / Sanders, R.W. / Ward, A.B. / Wilson, I.A.
History
DepositionAug 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
H: COVA2-39 heavy chain
L: COVA2-39 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7764
Polymers73,5553
Non-polymers2211
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-29 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.905, 80.445, 72.006
Angle α, β, γ (deg.)90.000, 104.880, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Spike protein S1


Mass: 26095.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody COVA2-39 heavy chain


Mass: 24710.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody COVA2-39 light chain


Mass: 22749.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 5.6 20% isopropanol 10% ethylene glycol 20% polyethylene glycol 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.712→50 Å / Num. obs: 79139 / % possible obs: 97.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.032 / Rrim(I) all: 0.066 / Χ2: 1.326 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.72-1.753.50.93439200.5060.5761.1030.46397.6
1.75-1.783.60.70339590.6840.4270.8270.41998
1.78-1.823.60.58539690.740.3510.6860.43798.1
1.82-1.853.60.4439750.8370.2620.5140.44298.5
1.85-1.893.60.36640080.8520.2190.4290.57798.1
1.89-1.943.40.33539210.8490.2120.3990.88996.4
1.94-1.993.60.22439530.9360.1360.2640.63398
1.99-2.043.60.17339970.9670.1050.2030.63197.5
2.04-2.13.30.15838630.9640.10.1880.9395.5
2.1-2.173.20.10937830.9830.0690.130.7992.8
2.17-2.243.70.10839130.9860.0630.1250.8997.2
2.24-2.333.60.11139510.9790.0670.1311.42997.2
2.33-2.4440.08339810.9910.0470.0961.16397.9
2.44-2.573.90.07639830.990.0440.0881.44397.4
2.57-2.733.80.06839660.9930.0390.0791.80797.7
2.73-2.943.70.05839580.9950.0340.0682.20296.9
2.94-3.243.50.04938540.9960.0290.0582.58694.5
3.24-3.7140.04540710.9970.0250.0512.90399.4
3.71-4.6740.0440550.9980.0210.0452.7998.5
4.67-503.80.03440590.9980.0180.0392.25996.8

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 1.712→34.824 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 3841 4.86 %
Rwork0.1768 75260 -
obs0.1783 79101 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.37 Å2 / Biso mean: 34.7183 Å2 / Biso min: 15.6 Å2
Refinement stepCycle: final / Resolution: 1.712→34.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 14 482 4926
Biso mean--84.38 42.25 -
Num. residues----594
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.712-1.73320.3261240.3088235582
1.7332-1.7560.30961430.2742283498
1.756-1.780.29621520.2486278698
1.78-1.80550.25061690.2308281498
1.8055-1.83240.2561690.2126281998
1.8324-1.8610.25541340.2009284398
1.861-1.89160.23021510.2149276098
1.8916-1.92420.26751560.2333275096
1.9242-1.95920.26031510.202284198
1.9592-1.99680.21391600.1875279198
1.9968-2.03760.19811340.1793277597
2.0376-2.08190.2221240.1863274995
2.0819-2.13030.20971640.1745266394
2.1303-2.18360.21521650.1746268694
2.1836-2.24260.23411430.1821280597
2.2426-2.30860.23021350.1879281997
2.3086-2.38310.20261490.1834279898
2.3831-2.46820.23151390.1701283398
2.4682-2.5670.18761280.1809281497
2.567-2.68380.2141180.1779282497
2.6838-2.82530.23841400.1828281398
2.8253-3.00220.21751330.1844280395
3.0022-3.23380.23451320.1858271795
3.2338-3.5590.21141330.1699291399
3.559-4.07330.20151020.1584293799
4.0733-5.12930.15481330.1379287698
5.1293-34.8240.17051600.1705284296
Refinement TLS params.Method: refined / Origin x: -37.9424 Å / Origin y: 9.8245 Å / Origin z: 20.2696 Å
111213212223313233
T0.2012 Å20.0024 Å20.0139 Å2-0.1765 Å2-0.0188 Å2--0.1684 Å2
L1.4 °20.0061 °20.1568 °2-0.1974 °2-0.0692 °2--0.49 °2
S-0.0034 Å °0.1973 Å °0.026 Å °-0.0339 Å °-0.0024 Å °0.044 Å °0.0518 Å °-0.0953 Å °0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA338 - 1001
2X-RAY DIFFRACTION1allH2 - 214
3X-RAY DIFFRACTION1allL3 - 209
4X-RAY DIFFRACTION1allS1 - 482

+
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