[English] 日本語
Yorodumi
- PDB-7x9e: Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 sp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x9e
TitleCrystal structure of the 76E1 Fab in complex with a SARS-CoV-2 spike peptide
Components
  • 76E1 Fab Heavy Chain
  • 76E1 Fab Light Chain
  • Spike peptide
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV-2 / Antibody / Fab / Spike / Fusion peptide / 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 / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / symbiont-mediated suppression of host innate immune response / structural constituent of virion ...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 / symbiont-mediated suppression of host innate immune response / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / 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 / 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, X. / Zhang, T. / Ding, J. / Sun, X. / Sun, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Microbiol / Year: 2022
Title: Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2.
Authors: Sun, X. / Yi, C. / Zhu, Y. / Ding, L. / Xia, S. / Chen, X. / Liu, M. / Gu, C. / Lu, X. / Fu, Y. / Chen, S. / Zhang, T. / Zhang, Y. / Yang, Z. / Ma, L. / Gu, W. / Hu, G. / Du, S. / Yan, R. / ...Authors: Sun, X. / Yi, C. / Zhu, Y. / Ding, L. / Xia, S. / Chen, X. / Liu, M. / Gu, C. / Lu, X. / Fu, Y. / Chen, S. / Zhang, T. / Zhang, Y. / Yang, Z. / Ma, L. / Gu, W. / Hu, G. / Du, S. / Yan, R. / Fu, W. / Yuan, S. / Qiu, C. / Zhao, C. / Zhang, X. / He, Y. / Qu, A. / Zhou, X. / Li, X. / Wong, G. / Deng, Q. / Zhou, Q. / Lu, H. / Ling, Z. / Ding, J. / Lu, L. / Xu, J. / Xie, Y. / Sun, B.
History
DepositionMar 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 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: 76E1 Fab Heavy Chain
B: 76E1 Fab Light Chain
C: 76E1 Fab Heavy Chain
D: 76E1 Fab Light Chain
E: Spike peptide
F: Spike peptide


Theoretical massNumber of molelcules
Total (without water)98,2266
Polymers98,2266
Non-polymers00
Water1,65792
1
A: 76E1 Fab Heavy Chain
B: 76E1 Fab Light Chain
E: Spike peptide


Theoretical massNumber of molelcules
Total (without water)49,1133
Polymers49,1133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-28 kcal/mol
Surface area18720 Å2
MethodPISA
2
C: 76E1 Fab Heavy Chain
D: 76E1 Fab Light Chain
F: Spike peptide


Theoretical massNumber of molelcules
Total (without water)49,1133
Polymers49,1133
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-28 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.356, 84.515, 87.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Antibody 76E1 Fab Heavy Chain


Mass: 23378.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 76E1 Fab Light Chain


Mass: 22949.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: Abvec-HIgG1 / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Spike peptide


Mass: 2785.198 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M sodium citrate pH 4.5, 20% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2021
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 30037 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Net I/σ(I): 18.8
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2953 / CC1/2: 0.534

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BQB

6bqb


Resolution: 2.6→38.88 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 1499 5 %
Rwork0.1949 28455 -
obs0.1974 29954 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.79 Å2 / Biso mean: 34.683 Å2 / Biso min: 13.53 Å2
Refinement stepCycle: final / Resolution: 2.6→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6530 0 0 92 6622
Biso mean---28.95 -
Num. residues----871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086690
X-RAY DIFFRACTIONf_angle_d1.0399103
X-RAY DIFFRACTIONf_chiral_restr0.0571033
X-RAY DIFFRACTIONf_plane_restr0.0071160
X-RAY DIFFRACTIONf_dihedral_angle_d15.1463984
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.601-2.68490.38641280.3234238392
2.6849-2.78090.37411310.2885255699
2.7809-2.89220.34691410.2703255599
2.8922-3.02380.30651360.25982572100
3.0238-3.18310.31861340.22782577100
3.1831-3.38240.27371350.20922605100
3.3824-3.64340.27641320.18422575100
3.6434-4.00970.18561430.16882595100
4.0097-4.58920.17811390.13272621100
4.5892-5.77880.15991380.14512657100
5.7788-38.880.20561420.1853275999
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)
11.9793-1.36340.25233.6995-0.21452.3728-0.0306-0.15210.07-0.07240.06280.18780.0677-0.011-0.05850.158-0.005-0.00390.15150.00580.214136.4118.576142.958
21.8928-0.1610.0322.35230.33973.00320.05150.0337-0.2352-0.0703-0.04590.38560.1093-0.4099-0.01750.24540.048-0.01790.39080.06130.3209126.9125.016107.471
32.7422-1.7549-1.01433.8580.71946.0032-0.1426-0.0498-0.1145-0.2673-0.15810.1773-0.258-0.33360.2910.2538-0.0133-0.02460.4290.03490.3882126.49225.192104.54
42.7695-0.47980.38042.1342-0.11253.65480.0902-0.1148-0.2421-0.1786-0.085-0.15610.31390.137-0.01410.19720.02780.02050.16060.06380.2516147.0282.926132.37
51.07730.224-0.17984.8979-0.11521.99990.0632-0.0388-0.03040.0143-0.1582-0.1658-0.14280.28730.09750.2138-0.00990.03920.33810.10670.2668142.92320.573107.873
63.6861.09670.22373.1226-0.40183.47190.16290.25130.26940.0891-0.2415-0.0385-0.27370.11820.05730.24610.04090.02020.22930.03570.1697172.5129.23281.488
72.03721.16860.42982.8667-1.36353.76-0.05850.0729-0.0299-0.04380.1162-0.07120.0418-0.2631-0.05560.1279-0.00180.00980.1902-0.04130.1894183.2249.06118.921
83.2170.2578-0.18441.3667-0.33974.27110.203-0.0137-0.25790.1873-0.01120.4106-0.0435-0.8735-0.16740.243-0.00920.0280.43790.02310.2977154.6812.93991.807
93.6741.49890.42522.97890.37143.3019-0.006-0.11880.33190.057-0.01410.1818-0.1396-0.38580.00260.22180.0374-0.0360.26870.00530.2092167.77715.138118.167
106.22170.3591.15844.72272.52935.03080.1398-0.31510.11770.89320.4038-0.28970.49270.7918-0.54620.31690.1298-0.03080.516-0.0090.2812148.8611.361153.368
114.1536-0.13791.57776.7263-1.65156.4810.21990.39380.4374-0.40990.1420.21290.19680.0662-0.36410.21750.10810.01780.5539-0.05140.3538158.598.55269.976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:121 )A2 - 121
2X-RAY DIFFRACTION2( CHAIN A AND RESID 122:175 )A122 - 175
3X-RAY DIFFRACTION3( CHAIN A AND RESID 176:223 )A176 - 223
4X-RAY DIFFRACTION4( CHAIN B AND RESID 3:110 )B3 - 110
5X-RAY DIFFRACTION5( CHAIN B AND RESID 111:213 )B111 - 213
6X-RAY DIFFRACTION6( CHAIN C AND RESID 2:119 )C2 - 119
7X-RAY DIFFRACTION7( CHAIN C AND RESID 120:223 )C120 - 223
8X-RAY DIFFRACTION8( CHAIN D AND RESID 3:110 )D3 - 110
9X-RAY DIFFRACTION9( CHAIN D AND RESID 111:212 )D111 - 212
10X-RAY DIFFRACTION10( CHAIN E AND RESID 814:825 )E814 - 825
11X-RAY DIFFRACTION11( CHAIN F AND RESID 812:826 )F812 - 826

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more