[English] 日本語
Yorodumi
- PDB-8tnt: Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tnt
TitleCrystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2
Components
  • (Envelope glycoprotein ...) x 2
  • 769C2 heavy chain
  • 769C2 light chain
  • F-2-1 heavy chain
  • F-2-1 light chain
  • Glycoprotein 42
KeywordsIMMUNE SYSTEM / Viral Protein / Antibody
Function / homology
Function and homology information


host cell membrane / host cell endosome membrane / carbohydrate binding / host cell Golgi apparatus / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / 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 / C-type lectin fold
Similarity search - Domain/homology
Glycoprotein 42 / Envelope glycoprotein L / Envelope glycoprotein H
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBu, W. / Kumar, A. / Board, N. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. ...Bu, W. / Kumar, A. / Board, N. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. / Pittaluga, S. / Marcotrigiano, J. / Cohen, J.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Immunity / Year: 2024
Title: Epstein-Barr virus gp42 antibodies reveal sites of vulnerability for receptor binding and fusion to B cells.
Authors: Bu, W. / Kumar, A. / Board, N.L. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. / Pittaluga, S. / Marcotrigiano, J. / Cohen, J.I.
History
DepositionAug 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Glycoprotein 42
D: 769C2 light chain
E: 769C2 heavy chain
F: F-2-1 light chain
G: F-2-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,2289
Polymers202,7857
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.317, 85.172, 119.714
Angle α, β, γ (deg.)90.00, 105.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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

#1: Protein Envelope glycoprotein H


Mass: 72687.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Gene: gH / Production host: Homo sapiens (human) / References: UniProt: P03231
#2: Protein Envelope glycoprotein L


Mass: 12475.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Gene: gL / Production host: Homo sapiens (human) / References: UniProt: P03212

-
Antibody , 4 types, 4 molecules DEFG

#4: Antibody 769C2 light chain


Mass: 22842.115 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 heavy chain


Mass: 24670.713 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 F-2-1 light chain


Mass: 23723.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#7: Antibody F-2-1 heavy chain


Mass: 24759.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 3 molecules C

#3: Protein Glycoprotein 42


Mass: 21626.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Gene: BZLF2 / Production host: Homo sapiens (human) / References: UniProt: P03205
#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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
Details: 20mM Tris pH7.5, 150mM NaCl, 4% Tacsimate pH 7.0, and 10% PEG 3,350
PH range: 7.0 - 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→47.28 Å / Num. obs: 39158 / % possible obs: 98.7 % / Redundancy: 1.9 % / Rsym value: 0.101 / Net I/σ(I): 7.4
Reflection shellResolution: 3.15→3.28 Å / Num. unique obs: 3913 / Rsym value: 0.767

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→46.32 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2866 1984 5.08 %
Rwork0.2545 --
obs0.2562 39052 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13703 0 28 0 13731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214062
X-RAY DIFFRACTIONf_angle_d0.56519171
X-RAY DIFFRACTIONf_dihedral_angle_d4.5231947
X-RAY DIFFRACTIONf_chiral_restr0.0412209
X-RAY DIFFRACTIONf_plane_restr0.0052435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.230.3791500.35332612X-RAY DIFFRACTION99
3.23-3.320.37791500.34712596X-RAY DIFFRACTION98
3.32-3.410.37991330.33212664X-RAY DIFFRACTION98
3.41-3.520.35671300.30892680X-RAY DIFFRACTION100
3.52-3.650.38791050.29342656X-RAY DIFFRACTION99
3.65-3.80.31491260.28452662X-RAY DIFFRACTION99
3.8-3.970.32511270.26112687X-RAY DIFFRACTION99
3.97-4.180.26841400.2422660X-RAY DIFFRACTION99
4.18-4.440.27221750.2182641X-RAY DIFFRACTION99
4.44-4.780.22641720.2142646X-RAY DIFFRACTION99
4.78-5.260.25461430.22412632X-RAY DIFFRACTION98
5.26-6.020.29091720.252677X-RAY DIFFRACTION100
6.02-7.580.26441270.26132728X-RAY DIFFRACTION100
7.58-46.320.23861340.20782527X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 2.7982 Å / Origin y: 4.6949 Å / Origin z: 44.211 Å
111213212223313233
T0.4457 Å2-0.0182 Å2-0.0042 Å2-0.3502 Å2-0.0009 Å2--0.2777 Å2
L0.9079 °2-0.2448 °20.3437 °2-0.3574 °2-0.0411 °2--0.5906 °2
S0.0113 Å °0.0167 Å °-0.1018 Å °-0.1015 Å °-0.0124 Å °0.0633 Å °-0.069 Å °-0.1262 Å °-0.0028 Å °
Refinement TLS groupSelection details: all

+
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