[English] 日本語
Yorodumi
- PDB-7s0j: Crystal structure of Epstein-Barr virus gH/gL targeting antibody ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s0j
TitleCrystal structure of Epstein-Barr virus gH/gL targeting antibody 769B10
Components
  • 769B10 Fab Heavy chain
  • 769B10 Fab Light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / gH/gL / Epstein-Barr virus / herpesvirus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, W.-H. / Kanekiyo, M. / Cohen, J.I. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAAI000978-13 United States
CitationJournal: Immunity / Year: 2022
Title: Epstein-Barr virus gH/gL has multiple sites of vulnerability for virus neutralization and fusion inhibition.
Authors: Chen, W.H. / Kim, J. / Bu, W. / Board, N.L. / Tsybovsky, Y. / Wang, Y. / Hostal, A. / Andrews, S.F. / Gillespie, R.A. / Choe, M. / Stephens, T. / Yang, E.S. / Pegu, A. / Peterson, C.E. / ...Authors: Chen, W.H. / Kim, J. / Bu, W. / Board, N.L. / Tsybovsky, Y. / Wang, Y. / Hostal, A. / Andrews, S.F. / Gillespie, R.A. / Choe, M. / Stephens, T. / Yang, E.S. / Pegu, A. / Peterson, C.E. / Fisher, B.E. / Mascola, J.R. / Pittaluga, S. / McDermott, A.B. / Kanekiyo, M. / Joyce, M.G. / Cohen, J.I.
History
DepositionAug 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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
L: 769B10 Fab Light chain
H: 769B10 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9004
Polymers48,7162
Non-polymers1842
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation, Purification by Protein A resin
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-25 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.174, 67.051, 65.030
Angle α, β, γ (deg.)90.000, 107.640, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody 769B10 Fab Light chain


Mass: 23452.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 769B10 Fab Heavy chain


Mass: 25264.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl pH8.0, 18% PEG5000MME, 0.2M NaCl, 2.5% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 28030 / % possible obs: 89.7 % / Redundancy: 4.5 % / CC1/2: 0.82 / Net I/σ(I): 5.3
Reflection shellResolution: 2.15→2.25 Å / Num. unique obs: 22877 / CC1/2: 0.72

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UV4

4uv4


Resolution: 2.15→41.83 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 1398 4.99 %
Rwork0.2353 26632 -
obs0.2366 28030 56.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.24 Å2 / Biso mean: 29.7535 Å2 / Biso min: 14.86 Å2
Refinement stepCycle: final / Resolution: 2.15→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 12 207 3609
Biso mean--35.37 27.78 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023491
X-RAY DIFFRACTIONf_angle_d0.5794738
X-RAY DIFFRACTIONf_dihedral_angle_d16.5251247
X-RAY DIFFRACTIONf_chiral_restr0.044525
X-RAY DIFFRACTIONf_plane_restr0.004608
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.230.3411460.322389293819
2.23-2.310.2989760.31231432150831
2.31-2.420.3475960.30621857195339
2.42-2.550.33591220.28532241236348
2.55-2.710.30811430.27412883302662
2.71-2.920.23491780.26233389356772
2.92-3.210.251910.23963581377277
3.21-3.670.23241840.21853534371875
3.67-4.630.28461700.20213256342669
4.63-41.830.23181920.21373567375976
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)
11.59690.51230.63021.92370.39871.3780.14430.1449-0.1472-0.05410.0892-0.1499-0.00830.3628-0.03560.21910.02660.0090.2576-0.05430.247227.6729.735-30.043
22.56830.67780.12830.9376-0.60361.2650.10640.13040.0989-0.27470.00260.1495-0.04180.1374-0.07030.22190.00570.03280.2492-0.05290.174224.45913.476-37.82
31.89780.68891.23280.60390.69070.87530.00010.233-0.65330.03580.0822-0.59390.0710.2782-0.04510.19350.00680.09170.2076-0.13630.101828.26617.053-29.038
43.73750.3031-0.9172.8847-0.07994.06740.2298-0.1234-0.02650.2457-0.2167-0.0796-0.2644-0.42410.04010.10360.0253-0.05370.14270.01160.120434.65733.241-4.132
52.98490.6677-1.22241.39780.15663.17740.03270.0624-0.0253-0.06240.0327-0.3203-0.1306-0.1071-0.02690.17140.02410.01940.1162-0.00340.166135.1425.904-9.097
62.966-0.4588-0.33532.01670.45333.3777-0.0983-0.29140.13470.39840.0503-0.23710.1790.1086-0.02360.2510.0165-0.03910.18760.00530.188838.53928.4452.18
72.12680.15921.03032.0567-0.28072.4755-0.13820.31920.0097-0.5712-0.42270.2625-0.76480.203-0.12230.32370.10930.03070.17810.03580.22014.65224.753-22.323
83.7780.2556-0.79013.725-0.44432.26340.07720.0854-0.2671-0.23120.02010.66890.3006-0.3459-0.05930.29580.048-0.020.20940.00610.30843.2914.003-26.653
91.128-0.1726-0.82391.72560.90780.7947-0.12460.0080.02610.5567-0.18440.48490.4977-0.1683-0.16630.2702-0.00950.07110.20760.00380.20148.52916.741-21.304
100.63121.03910.2581.93770.42970.71460.0416-0.0662-0.0889-0.11350.0764-0.1719-0.12330.07920.02980.12490.118-0.06140.1835-0.01880.177918.24123.402-20.385
113.18391.4048-0.20470.484-0.19070.68370.0826-0.06980.3944-0.0873-0.02470.31260.022-0.20470.05310.24510.00760.00620.1781-0.04010.181224.94740.512-9.084
123.73171.3324-0.51042.90750.26781.64950.45620.03860.31750.7101-0.08330.0999-0.4810.0020.17620.19350.0271-0.00920.19520.01890.072329.56737.745-10.392
134.03472.16050.63383.37910.75232.1759-0.3232-0.61661.5233-0.1024-0.0330.6514-0.6111-0.03860.01150.2754-0.0130.01310.1516-0.09760.255726.62947.967-6.516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN L AND RESID 1:38 )L1 - 38
2X-RAY DIFFRACTION2( CHAIN L AND RESID 39:75 )L39 - 75
3X-RAY DIFFRACTION3( CHAIN L AND RESID 76:113 )L76 - 113
4X-RAY DIFFRACTION4( CHAIN L AND RESID 114:143 )L114 - 143
5X-RAY DIFFRACTION5( CHAIN L AND RESID 144:174 )L144 - 174
6X-RAY DIFFRACTION6( CHAIN L AND RESID 175:213 )L175 - 213
7X-RAY DIFFRACTION7( CHAIN H AND RESID 1:17 )H1 - 17
8X-RAY DIFFRACTION8( CHAIN H AND RESID 18:82 )H18 - 82
9X-RAY DIFFRACTION9( CHAIN H AND RESID 83:97 )H83 - 97
10X-RAY DIFFRACTION10( CHAIN H AND RESID 98:131 )H98 - 131
11X-RAY DIFFRACTION11( CHAIN H AND RESID 132:154 )H132 - 154
12X-RAY DIFFRACTION12( CHAIN H AND RESID 155:185 )H155 - 185
13X-RAY DIFFRACTION13( CHAIN H AND RESID 186:211 )H186 - 211

+
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