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- PDB-1wiq: STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, TRIGONAL CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 1wiq
TitleSTRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, TRIGONAL CRYSTAL FORM
ComponentsT-CELL SURFACE GLYCOPROTEIN CD4
KeywordsGLYCOPROTEIN / IMMUNOGLOBULIN FOLD / TRANSMEMBRANE / T-CELL / MHC LIPOPROTEIN / POLYMORPHISM
Function / homology
Function and homology information


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / positive regulation of interleukin-2 production / protein tyrosine kinase binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / early endosome / cell adhesion / positive regulation of protein phosphorylation / immune response / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / lipid binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 ...CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT PLUS ANOMALOUS DIFFRACTION. / Resolution: 5 Å
AuthorsWu, H. / Kwong, P.D. / Hendrickson, W.A.
CitationJournal: Nature / Year: 1997
Title: Dimeric association and segmental variability in the structure of human CD4.
Authors: Wu, H. / Kwong, P.D. / Hendrickson, W.A.
History
DepositionDec 18, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-CELL SURFACE GLYCOPROTEIN CD4
B: T-CELL SURFACE GLYCOPROTEIN CD4


Theoretical massNumber of molelcules
Total (without water)80,9112
Polymers80,9112
Non-polymers00
Water00
1
A: T-CELL SURFACE GLYCOPROTEIN CD4


Theoretical massNumber of molelcules
Total (without water)40,4551
Polymers40,4551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T-CELL SURFACE GLYCOPROTEIN CD4


Theoretical massNumber of molelcules
Total (without water)40,4551
Polymers40,4551
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.000, 126.000, 205.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHERE ARE TWO MOLECULES PER CRYSTALLOGRAPHIC ASYMMETRIC UNIT. EACH MOLECULE CONTAINS RESIDUES 1 - 363.

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Components

#1: Protein T-CELL SURFACE GLYCOPROTEIN CD4 / CD4


Mass: 40455.477 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR FRAGMENT / Source method: isolated from a natural source / Details: TRIGONAL CRYSTAL FORM / Source: (natural) Homo sapiens (human) / References: UniProt: P01730

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.81 Å3/Da / Density % sol: 78.81 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.2 / Method: vapor diffusion, hanging drop
Details: Kwong, P.D., (1990) Proc. Natl. Acad. Sci. U.S.A., 87, 6423.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.23 %PEG4001drop
2183 mMammonium phosphate1drop
340 mMsodium phosphate1drop
410 mMTris-HCl1drop
53.1 mM1dropNH4Cl
64.0 mg/mlsCD41drop
739.0 %satammonium sulfate1reservoir
8100 mMTris-HCl1reservoir
974 mM1reservoirNH4OH

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 5 Å / Lowest resolution: 8 Å / Num. obs: 4289 / % possible obs: 67.3 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 49.9 % / Rmerge(I) obs: 0.295

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Processing

Software
NameClassification
DENZOdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT PLUS ANOMALOUS DIFFRACTION.
Resolution: 5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.442 --
Rwork0.422 --
obs0.422 4289 67.3 %
Refinement stepCycle: LAST / Resolution: 5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5624 0 0 0 5624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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