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- PDB-1vlk: STRUCTURE OF VIRAL INTERLEUKIN-10 -

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Basic information

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


symbiont-mediated suppression of host pro-inflammatory cytokine signaling / symbiont-mediated activation of host anti-inflammatory cytokine signaling / symbiont-mediated suppression of host interferon-mediated signaling pathway / cytokine activity / immune response / extracellular space
Similarity search - Function
Interleukin-10 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / 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
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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
Has protein modificationY
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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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 %

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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

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