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- PDB-1wio: STRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, TETRAGONAL CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 1wio
TitleSTRUCTURE OF T-CELL SURFACE GLYCOPROTEIN CD4, TETRAGONAL CRYSTAL FORM
ComponentsT-CELL SURFACE GLYCOPROTEIN CD4
KeywordsGLYCOPROTEIN / IMMUNOGLOBULIN FOLD / TRANSMEMBRANE / T-CELL / MHC LIPOPROTEIN
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 / interleukin-15-mediated signaling pathway / regulation of T cell activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation ...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 / interleukin-15-mediated signaling pathway / regulation of T cell activation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of monocyte differentiation / positive regulation of kinase activity / Nef Mediated CD4 Down-regulation / Alpha-defensins / extracellular matrix structural constituent / T cell receptor complex / 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 / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / T cell activation / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / transmembrane signaling receptor activity / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / MHC class II protein complex binding / Clathrin-mediated endocytosis / signaling receptor activity / virus 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 ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / cell adhesion / immune response / positive regulation of protein phosphorylation / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
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: 3.9 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
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

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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)127.100, 127.100, 221.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
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: TETRAGONAL CRYSTAL FORM / Source: (natural) Homo sapiens (human) / References: UniProt: P01730
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.52 Å3/Da / Density % sol: 77.72 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / 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
11.4 %PEG4001drop
210.7 mMammonium sulfate1drop
34.3 mMsodium cacodylate1drop
43.6 mMTris-HCl1drop
51.2 mM1drop(NH4)3BO3
62.2 mg/mlsCD41drop
740.0 %PEG4001reservoir
8100 mMTris-HCl1reservoir
949.3 mM1reservoirNH4OH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 3.9 Å / Lowest resolution: 8 Å / Num. obs: 11993 / % possible obs: 80 % / Rmerge(I) obs: 0.112
Reflection shell
*PLUS
% possible obs: 53.8 % / Rmerge(I) obs: 0.34

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT PLUS ANOMALOUS DIFFRACTION.
Resolution: 3.9→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.351 --
Rwork0.24 --
obs0.24 11993 80 %
Refinement stepCycle: LAST / Resolution: 3.9→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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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