[English] 日本語
Yorodumi
- PDB-7d5z: Crystal structure of EBV gH/gL bound with neutralizing antibody 1D8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d5z
TitleCrystal structure of EBV gH/gL bound with neutralizing antibody 1D8
Components
  • Envelope glycoprotein H
  • Envelope glycoprotein L
  • heavy chain of 1D8
  • light chain of 1D8
KeywordsVIRAL PROTEIN / EBV gH/gL / antibody
Function / homology
Function and homology information


host cell endosome membrane / host cell Golgi apparatus / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane
Similarity search - Function
Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain
Similarity search - Domain/homology
Envelope glycoprotein H / Envelope glycoprotein L
Similarity search - Component
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsZhu, Q. / Shan, S. / Yu, J. / Wang, X. / Zhang, L. / Zeng, M.
CitationJournal: To Be Published
Title: A Neutralizing Antibody Targeting a New Site of Vulnerability on Epstein-Barr Virus gH/gL Protects against Dual-Tropic Infection
Authors: Zhu, Q. / Shan, S. / Yu, J. / Wang, X. / Zhang, L. / Zeng, M.
History
DepositionSep 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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
M: Envelope glycoprotein H
N: Envelope glycoprotein L
O: light chain of 1D8
P: heavy chain of 1D8
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: light chain of 1D8
D: heavy chain of 1D8
E: Envelope glycoprotein H
F: Envelope glycoprotein L
G: light chain of 1D8
H: heavy chain of 1D8
I: Envelope glycoprotein H
J: Envelope glycoprotein L
K: light chain of 1D8
L: heavy chain of 1D8


Theoretical massNumber of molelcules
Total (without water)653,99216
Polymers653,99216
Non-polymers00
Water0
1
M: Envelope glycoprotein H
N: Envelope glycoprotein L
O: light chain of 1D8
P: heavy chain of 1D8


Theoretical massNumber of molelcules
Total (without water)163,4984
Polymers163,4984
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: light chain of 1D8
D: heavy chain of 1D8


Theoretical massNumber of molelcules
Total (without water)163,4984
Polymers163,4984
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Envelope glycoprotein H
F: Envelope glycoprotein L
G: light chain of 1D8
H: heavy chain of 1D8


Theoretical massNumber of molelcules
Total (without water)163,4984
Polymers163,4984
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Envelope glycoprotein H
J: Envelope glycoprotein L
K: light chain of 1D8
L: heavy chain of 1D8


Theoretical massNumber of molelcules
Total (without water)163,4984
Polymers163,4984
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.865, 212.865, 598.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
Envelope glycoprotein H / gH


Mass: 73959.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Gene: gH, BXLF2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q3KSQ3
#2: Protein
Envelope glycoprotein L / gL


Mass: 12491.126 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Gene: gL, BKRF2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q3KSS3
#3: Antibody
light chain of 1D8


Mass: 25496.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Protein
heavy chain of 1D8


Mass: 51550.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.18 Å3/Da / Density % sol: 76.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200 mM Sodium Citrate, 100 mM HEPES Sodium Salt, pH 7.5, 15 % w/v MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 4.2→50.08 Å / Num. obs: 100776 / % possible obs: 99.34 % / Redundancy: 8.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Net I/σ(I): 8
Reflection shellResolution: 4.2→4.35 Å / Num. unique obs: 9853 / CC1/2: 0.997

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5t1d

5t1d


Resolution: 4.2→50.03 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 5078 5.06 %RANDOM
Rwork0.2458 95245 --
obs0.2474 100323 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 434.83 Å2 / Biso mean: 153.1349 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 4.2→50.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36304 0 0 0 36304
Num. residues----4704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2-4.250.38221590.36113094325397
4.25-4.30.35321480.343131223270100
4.3-4.350.36561610.332331673328100
4.35-4.410.33222040.324130873291100
4.41-4.460.33571630.304431553318100
4.46-4.530.27531500.28731783328100
4.53-4.590.3131600.281631403300100
4.59-4.660.29821580.285431543312100
4.66-4.730.28711790.270931573336100
4.73-4.810.30771610.281831563317100
4.81-4.890.26361760.265531223298100
4.89-4.980.31681590.260231733332100
4.98-5.080.29421580.259431933351100
5.08-5.180.31071820.253831653347100
5.18-5.290.28141760.255731263302100
5.29-5.410.28611870.253331443331100
5.41-5.550.30611690.264631693338100
5.55-5.70.32591470.263532103357100
5.7-5.870.29771540.263731983352100
5.87-6.060.30651660.266731753341100
6.06-6.270.33341830.267732023385100
6.27-6.520.28181780.255131683346100
6.52-6.820.30041500.246232303380100
6.82-7.180.26851810.240531983379100
7.18-7.630.2651720.22532223394100
7.63-8.210.23831770.212132293406100
8.21-9.030.22561810.18143220340199
9.04-10.330.18681800.15983256343699
10.33-12.980.19971710.16553210338197
12.98-50.030.30161880.26873225341392

+
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