[English] 日本語
Yorodumi
- PDB-8too: Crystal structure of Epstein-Barr virus gp42 in complex with anti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8too
TitleCrystal structure of Epstein-Barr virus gp42 in complex with antibody 4C12
Components
  • 4C12 heavy chain
  • 4C12 light chain
  • Glycoprotein 42
KeywordsIMMUNE SYSTEM / Viral Protein / Antibody
Function / homologyC-type lectin-like/link domain superfamily / host cell membrane / C-type lectin fold / carbohydrate binding / virion membrane / membrane / Glycoprotein 42
Function and homology information
Biological speciesMus musculus (house mouse)
Epstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4C12 light chain
B: 4C12 heavy chain
C: 4C12 light chain
D: 4C12 heavy chain
E: 4C12 light chain
F: 4C12 light chain
G: 4C12 heavy chain
H: 4C12 heavy chain
I: Glycoprotein 42
J: Glycoprotein 42
K: Glycoprotein 42
L: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)258,81712
Polymers258,81712
Non-polymers00
Water3,441191
1
A: 4C12 light chain
B: 4C12 heavy chain
I: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)64,7043
Polymers64,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 4C12 light chain
D: 4C12 heavy chain
J: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)64,7043
Polymers64,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 4C12 light chain
H: 4C12 heavy chain
L: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)64,7043
Polymers64,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: 4C12 light chain
G: 4C12 heavy chain
K: Glycoprotein 42


Theoretical massNumber of molelcules
Total (without water)64,7043
Polymers64,7043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.296, 63.568, 199.278
Angle α, β, γ (deg.)89.81, 89.75, 88.86
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody
4C12 light chain


Mass: 23604.100 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
4C12 heavy chain


Mass: 25154.045 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein
Glycoprotein 42


Mass: 15946.102 Da / Num. of mol.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM Tris pH7.5, 150mM NaCl, 0.2M zinc acetate dihydrate, and 18% PEG 3,350

-
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: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→66.42 Å / Num. obs: 73888 / % possible obs: 91.8 % / Redundancy: 3.8 % / Rsym value: 0.157 / Net I/σ(I): 5.4
Reflection shellResolution: 2.6→2.6 Å / Num. unique obs: 7047 / Rsym value: 1.187

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→53.51 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 3745 5.08 %
Rwork0.2256 --
obs0.2281 73652 91.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→53.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17022 0 0 191 17213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417488
X-RAY DIFFRACTIONf_angle_d0.81623901
X-RAY DIFFRACTIONf_dihedral_angle_d4.6172438
X-RAY DIFFRACTIONf_chiral_restr0.0512703
X-RAY DIFFRACTIONf_plane_restr0.0063047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.38061160.30652538X-RAY DIFFRACTION87
2.63-2.670.32751180.30132439X-RAY DIFFRACTION85
2.67-2.70.35211490.32256X-RAY DIFFRACTION83
2.7-2.740.43551040.28022239X-RAY DIFFRACTION78
2.74-2.780.33911480.27422584X-RAY DIFFRACTION91
2.78-2.830.33491400.2492673X-RAY DIFFRACTION95
2.83-2.870.32281250.25192687X-RAY DIFFRACTION95
2.87-2.920.31261370.25662708X-RAY DIFFRACTION95
2.92-2.980.34251370.25972701X-RAY DIFFRACTION95
2.98-3.030.34161400.262688X-RAY DIFFRACTION95
3.03-3.10.29641480.24362636X-RAY DIFFRACTION94
3.1-3.160.33511510.25362697X-RAY DIFFRACTION94
3.16-3.240.36931250.25482640X-RAY DIFFRACTION95
3.24-3.320.28551550.23662695X-RAY DIFFRACTION94
3.32-3.410.25231790.2242557X-RAY DIFFRACTION94
3.41-3.510.32961480.2212649X-RAY DIFFRACTION93
3.51-3.620.29551480.22862541X-RAY DIFFRACTION91
3.62-3.750.29981370.23272534X-RAY DIFFRACTION89
3.75-3.90.26471160.22292441X-RAY DIFFRACTION86
3.9-4.080.25761050.20012345X-RAY DIFFRACTION82
4.08-4.290.25491570.18472709X-RAY DIFFRACTION97
4.29-4.560.19581780.17632725X-RAY DIFFRACTION97
4.56-4.910.20521500.17142719X-RAY DIFFRACTION96
4.91-5.410.23641370.19252673X-RAY DIFFRACTION95
5.41-6.190.29161190.22382702X-RAY DIFFRACTION95
6.19-7.790.25131390.24732412X-RAY DIFFRACTION85
7.79-53.510.24171390.23722719X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 4.1318 Å / Origin y: -18.8885 Å / Origin z: 8.2062 Å
111213212223313233
T0.1289 Å20.0436 Å20.0162 Å2-0.5478 Å20.0904 Å2--0.3208 Å2
L-0.0109 °20.0094 °2-0.0379 °2-0.0387 °2-0.0162 °2--0.1162 °2
S0.0049 Å °-0.0113 Å °-0.0214 Å °0.0034 Å °0.0146 Å °-0.0025 Å °0.0024 Å °0.0152 Å °-0.0212 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://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