[English] 日本語
Yorodumi
- PDB-1vlk: STRUCTURE OF VIRAL INTERLEUKIN-10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vlk
TitleSTRUCTURE OF VIRAL INTERLEUKIN-10
ComponentsVIRAL INTERLEUKIN-10
KeywordsCYTOKINE / GLYCOPROTEIN
Function / homology
Function and homology information


regulation of cytokine production / cytokine activity / immune response / virus-mediated perturbation of host defense response / extracellular space
Similarity search - Function
Interleukin-10 / Interleukin-10 family / Interleukin-10/19/20/22/24/26 family / Interleukin 10 / Interleukin-10, conserved site / Interleukin-10 family signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Viral interleukin-10 homolog
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsZdanov, A. / Schalk-Hihi, C. / Wlodawer, A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of Epstein-Barr virus protein BCRF1, a homolog of cellular interleukin-10.
Authors: Zdanov, A. / Schalk-Hihi, C. / Menon, S. / Moore, K.W. / Wlodawer, A.
#1: Journal: Protein Sci. / Year: 1996
Title: Crystal Structure of Human Interleukin-10 at 1.6 A Resolution and a Model of a Complex with its Soluble Receptor
Authors: Zdanov, A. / Schalk-Hihi, C. / Wlodawer, A.
#2: Journal: Structure / Year: 1995
Title: Crystal Structure of Interleukin-10 Reveals the Functional Dimer with an Unexpected Topological Similarity to Interferon Gamma
Authors: Zdanov, A. / Schalk-Hihi, C. / Gustchina, A. / Tsang, M. / Weatherbee, J. / Wlodawer, A.
History
DepositionFeb 14, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VIRAL INTERLEUKIN-10


Theoretical massNumber of molelcules
Total (without water)17,1631
Polymers17,1631
Non-polymers00
Water1,35175
1
A: VIRAL INTERLEUKIN-10

A: VIRAL INTERLEUKIN-10


Theoretical massNumber of molelcules
Total (without water)34,3252
Polymers34,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area8700 Å2
ΔGint-81 kcal/mol
Surface area13830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)36.270, 36.270, 219.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE FUNCTIONAL MOLECULE IS A DIMER.

-
Components

#1: Protein VIRAL INTERLEUKIN-10 / BCRF1 PROTEIN


Mass: 17162.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Genus: Lymphocryptovirus / Strain: GD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03180
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS USE THE NUMBERING SCHEME OF HUMAN INTERLEUKIN-10 IN ACCORDANCE WITH THE SEQUENCE ...THE DEPOSITORS USE THE NUMBERING SCHEME OF HUMAN INTERLEUKIN-10 IN ACCORDANCE WITH THE SEQUENCE ALIGNMENT PROVIDED IN FIG.1 OF THEIR PAPER.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
23.4 mg/mlPEG40001drop
30.02 Msodium acetate1drop
40.04 Mammonium sulfate1drop
514 %PEG40001reservoir
60.1 Msodium acetate1reservoir
70.2 Mammonium sulfate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 4, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 9860 / % possible obs: 82 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.081
Reflection
*PLUS
Highest resolution: 1.9 Å
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 47 %

-
Processing

Software
NameClassification
DENZOdata reduction
PROFFTrefinement
RefinementResolution: 1.9→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.191 -
obs-9860
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 0 75 1193
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.052
X-RAY DIFFRACTIONp_angle_d0.0520.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0620.055
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4592.5
X-RAY DIFFRACTIONp_mcangle_it4.0753.5
X-RAY DIFFRACTIONp_scbond_it5.9384
X-RAY DIFFRACTIONp_scangle_it9.2877
X-RAY DIFFRACTIONp_plane_restr0.0120.022
X-RAY DIFFRACTIONp_chiral_restr0.190.18
X-RAY DIFFRACTIONp_singtor_nbd0.2250.5
X-RAY DIFFRACTIONp_multtor_nbd0.2480.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.250.5
X-RAY DIFFRACTIONp_planar_tor2.13.5
X-RAY DIFFRACTIONp_staggered_tor21.914
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.212
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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