[English] 日本語
Yorodumi
- PDB-7s1b: Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7s1b
TitleCrystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with human neutralizing antibodies 769C2 and 770F7
Components
  • (Envelope glycoprotein ...) x 2
  • 769C2 Fab heavy chain
  • 769C2 Fab light chain
  • 770F7 Fab heavy chain
  • 770F7 Fab light chain
  • Soluble gp42
KeywordsIMMUNE SYSTEM / Antibody / Fab / gH/gL / Epstein-Barr virus / herpesvirus
Function / homology
Function and homology information


host cell endosome membrane / carbohydrate binding / host cell Golgi apparatus / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / C-type lectin-like/link domain superfamily ...Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / C-type lectin-like/link domain superfamily / C-type lectin fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein L / Envelope glycoprotein H / Glycoprotein 42
Similarity search - Component
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsChen, W.-H. / Cohen, J.I. / Kanekiyo, M. / 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
DepositionSep 2, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
H: 770F7 Fab heavy chain
L: 770F7 Fab light chain
X: 769C2 Fab heavy chain
Y: 769C2 Fab light chain
C: Soluble gp42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,64011
Polymers183,7557
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Purification the protein complex by gel filtration (S200 column)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18990 Å2
ΔGint-100 kcal/mol
Surface area70940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.326, 107.703, 110.650
Angle α, β, γ (deg.)90.000, 93.110, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Envelope glycoprotein ... , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein H / gH


Mass: 72838.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Gene: gH, BXLF2 / Production host: Homo sapiens (human) / References: UniProt: P03231
#2: Protein Envelope glycoprotein L / gL


Mass: 12503.114 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Gene: gL, BKRF2 / Production host: Homo sapiens (human) / References: UniProt: P03212

-
Antibody , 4 types, 4 molecules HLXY

#3: Antibody 770F7 Fab heavy chain


Mass: 24626.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody 770F7 Fab light chain


Mass: 23397.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody 769C2 Fab heavy chain


Mass: 23840.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody 769C2 Fab light chain


Mass: 22782.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein/peptide / Sugars , 2 types, 5 molecules C

#7: Protein/peptide Soluble gp42


Mass: 3766.208 Da / Num. of mol.: 1 / Fragment: Residues 47-79
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Gene: BZLF2 / Production host: Homo sapiens (human) / References: UniProt: P0C6Z5
#8: 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.: 4
Source method: isolated from a genetically manipulated source
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES pH7.4, 24% PEG3350, 7.5% 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: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→71.32 Å / Num. obs: 40453 / % possible obs: 89.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 30.02 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.1
Reflection shellResolution: 3→3.1 Å / Num. unique obs: 2692 / CC1/2: 0.77

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W0K

5w0k


Resolution: 3.03→71.32 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.288 2005 5.49 %
Rwork0.2409 34536 -
obs0.2436 36541 89.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.49 Å2 / Biso mean: 46.8968 Å2 / Biso min: 6.21 Å2
Refinement stepCycle: final / Resolution: 3.03→71.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12201 0 56 0 12257
Biso mean--50.43 --
Num. residues----1596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.03-3.110.3765900.36741710180062
3.11-3.190.43051250.34772076220176
3.19-3.290.35731150.31162207232281
3.29-3.390.35221500.29752245239583
3.39-3.510.32541390.26592368250786
3.51-3.650.29341550.26312505266091
3.65-3.820.31231490.24692516266593
3.82-4.020.29841440.22732604274895
4.02-4.270.25411540.20482648280296
4.27-4.60.22611550.18672674282998
4.6-5.070.23531530.18752708286198
5.07-5.80.25091550.20912728288399
5.8-7.310.27141630.24612758292199
7.31-71.320.25281580.2172789294799
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)
11.27510.2736-0.3380.927-0.4560.41730.1285-0.0207-0.15440.0134-0.1149-0.0534-0.06280.00890.00690.1139-0.0148-0.03020.09950.03690.0295-0.4654.183-1.791
21.4414-0.27080.41950.9273-0.25370.9963-0.0453-0.0789-0.2797-0.10290.01210.3610.3802-0.0602-0.0044-0.12410.0049-0.08050.37460.21320.8253-48.683-10.38211.967
30.1397-0.10630.10130.5332-0.31110.77990.07870.0951-0.0936-0.4821-0.2156-0.06360.114-0.01690.00240.55540.1126-0.02440.1694-0.0119-0.48038.86126.278-49.402
40.2846-0.23130.08250.567-0.40030.9759-0.1205-0.01470.1278-0.0498-0.1564-0.0592-0.14470.12380.11330.52280.0231-0.07850.09430.0576-0.00089.66545.18-47.531
50.0645-0.0388-0.20080.01360.08250.4465-0.1141-0.0852-0.0569-0.04540.04470.01980.2056-0.00830.08720.5941-0.0934-0.0580.95260.34690.8755-53.345-26.4350.282
60.0469-0.0001-0.02850.0845-0.00250.0042-0.0079-0.33730.02790.22810.0069-0.0287-0.08850.0255-0.04530.6475-0.08320.12281.09850.30980.917-67.003-13.5457.896
71.48390.5923-0.11030.4980.15860.2280.0071-0.24150.18560.1427-0.09470.2134-0.011-0.15960.00740.17680.08860.15890.16950.05990.3572-4.66622.7853.552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:674 )A18 - 674
2X-RAY DIFFRACTION2( CHAIN B AND RESID 26:124 )B26 - 124
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:226 )H1 - 226
4X-RAY DIFFRACTION4( CHAIN L AND RESID 1:215 )L1 - 215
5X-RAY DIFFRACTION5( CHAIN X AND RESID 9:210 )X9 - 210
6X-RAY DIFFRACTION6( CHAIN Y AND RESID 2:213 )Y2 - 213
7X-RAY DIFFRACTION7( CHAIN C AND RESID 47:79 )C47 - 79

+
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