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- PDB-3cd4: REFINEMENT AND ANALYSIS OF THE FIRST TWO DOMAINS OF HUMAN CD4 -

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Basic information

Entry
Database: PDB / ID: 3cd4
TitleREFINEMENT AND ANALYSIS OF THE FIRST TWO DOMAINS OF HUMAN CD4
ComponentsT CELL SURFACE GLYCOPROTEIN CD4
KeywordsT-CELL SURFACE GLYCOPROTEIN
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 / 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 / Resolution: 2.2 Å
AuthorsGarrett, T.P.J. / Wang, J. / Yan, Y. / Harrison, S.C.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refinement and analysis of the structure of the first two domains of human CD4
Authors: Garrett, T.P.J. / Wang, J. / Yan, Y. / Liu, J. / Harrison, S.C.
#1: Journal: Nature / Year: 1990
Title: Atomic Structure of a Fragment of Human Cd4 Containing Two Immunoglobulin-Like Domains
Authors: Wang, J. / Yan, Y. / Garrett, T.P.J. / Liu, J. / Rodgers, D. / Garlick, R.L. / Tarr, G.E. / Husain, Y. / Reinherz, E.L. / Harrison, S.C.
History
DepositionJul 30, 1992Processing site: BNL
SupersessionOct 15, 1993ID: 2CD4
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET RESIDUES 89 - 102 FORM ONE UNINTERRUPTED STRAND PASSING FROM DOMAIN 1 TO DOMAIN 2. RESIDUES ...SHEET RESIDUES 89 - 102 FORM ONE UNINTERRUPTED STRAND PASSING FROM DOMAIN 1 TO DOMAIN 2. RESIDUES 89 - 98 FORM STRAND 2 OF SHEET *S1* AND RESIDUES 99 - 103 FORM STRAND 1 OF SHEET *S4*.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T CELL SURFACE GLYCOPROTEIN CD4


Theoretical massNumber of molelcules
Total (without water)20,2011
Polymers20,2011
Non-polymers00
Water54030
1
A: T CELL SURFACE GLYCOPROTEIN CD4

A: T CELL SURFACE GLYCOPROTEIN CD4


Theoretical massNumber of molelcules
Total (without water)40,4022
Polymers40,4022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)84.230, 30.650, 88.940
Angle α, β, γ (deg.)90.00, 118.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody T CELL SURFACE GLYCOPROTEIN CD4


Mass: 20200.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: OVARY / References: UniProt: P01730
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.197 / Rfactor obs: 0.197 / Highest resolution: 2.2 Å
Details: THE SIDE CHAINS OF RESIDUES 72 AND 73 HAVE BEEN INCLUDED IN TWO ALTERNATE CONFORMATIONS AND THE SIDE CHAIN OF RESIDUE 43 HAS BEEN INCLUDED AT 0.5 OCCUPANCY. THE ELECTRON DENSITY SUGGESTS ...Details: THE SIDE CHAINS OF RESIDUES 72 AND 73 HAVE BEEN INCLUDED IN TWO ALTERNATE CONFORMATIONS AND THE SIDE CHAIN OF RESIDUE 43 HAS BEEN INCLUDED AT 0.5 OCCUPANCY. THE ELECTRON DENSITY SUGGESTS THAT RESIDUE 43 MAY HAVE MORE THAN TWO ALTERNATE CONFORMATIONS. IN THE ELECTRON DENSITY MAP RESIDUES 20 - 23, 105 - 107 AND 132 - 137 APPEAR DISORDERED AND THEIR POSITIONS ARE UNRELIABLE. FOR RESIDUES 1, 40, 43, 87, 88, 89, AND 152 SIDE CHAIN POSITIONS ARE SOMEWHAT UNCERTAIN AS INDICATED BY LARGE B VALUES.
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 0 30 1420
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_deg2.42
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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