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- PDB-1cid: CRYSTAL STRUCTURE OF DOMAINS 3 & 4 OF RAT CD4 AND THEIR RELATIONS... -

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Basic information

Entry
Database: PDB / ID: 1cid
TitleCRYSTAL STRUCTURE OF DOMAINS 3 & 4 OF RAT CD4 AND THEIR RELATIONSHIP TO THE NH2-TERMINAL DOMAINS
ComponentsT CELL SURFACE GLYCOPROTEIN CD4
KeywordsT-CELL SURFACE GLYCOPROTEIN
Function / homology
Function and homology information


Translocation of ZAP-70 to Immunological synapse / Generation of second messenger molecules / PD-1 signaling / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / Phosphorylation of CD3 and TCR zeta chains / Other interleukin signaling / Alpha-defensins / interleukin-16 receptor activity / interleukin-16 binding ...Translocation of ZAP-70 to Immunological synapse / Generation of second messenger molecules / PD-1 signaling / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / Phosphorylation of CD3 and TCR zeta chains / Other interleukin signaling / Alpha-defensins / interleukin-16 receptor activity / interleukin-16 binding / induction by virus of host cell-cell fusion / maintenance of protein location in cell / T cell selection / MHC class II protein binding / positive regulation of monocyte differentiation / response to vitamin D / positive regulation of viral entry into host cell / interleukin-15-mediated signaling pathway / positive regulation of calcium ion transport into cytosol / coreceptor activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / macrophage differentiation / T cell differentiation / immunoglobulin binding / positive regulation of protein kinase activity / protein tyrosine kinase binding / positive regulation of T cell proliferation / T cell activation / response to estradiol / positive regulation of I-kappaB kinase/NF-kappaB signaling / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cell adhesion / membrane raft / external side of plasma membrane / signaling receptor binding / protein kinase binding / positive regulation of transcription, DNA-templated / integral component of plasma membrane / protein homodimerization activity / zinc ion binding / plasma membrane
Immunoglobulin C2-set domain / Immunoglobulin-like domain superfamily / T cell CD4 receptor C-terminal region / CD4, extracellular / Immunoglobulin-like fold / Immunoglobulin / Immunoglobulin V-set domain / Immunoglobulin C2-set / Immunoglobulin-like domain / Immunoglobulin subtype ...Immunoglobulin C2-set domain / Immunoglobulin-like domain superfamily / T cell CD4 receptor C-terminal region / CD4, extracellular / Immunoglobulin-like fold / Immunoglobulin / Immunoglobulin V-set domain / Immunoglobulin C2-set / Immunoglobulin-like domain / Immunoglobulin subtype / T-cell surface antigen CD4 / CD4, extracellular / T cell CD4 receptor C terminal region / Immunoglobulin domain / Ig-like domain profile.
T-cell surface glycoprotein CD4
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBrady, R.L. / Dodson, E.J. / Lange, G.
CitationJournal: Science / Year: 1993
Title: Crystal structure of domains 3 and 4 of rat CD4: relation to the NH2-terminal domains.
Authors: Brady, R.L. / Dodson, E.J. / Dodson, G.G. / Lange, G. / Davis, S.J. / Williams, A.F. / Barclay, A.N.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 28, 1993-
Revision 1.0Jul 15, 1993Provider: 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

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Assembly

Deposited unit
A: T CELL SURFACE GLYCOPROTEIN CD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8022
Polymers19,7061
Non-polymers961
Water25214
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)77.800, 77.800, 82.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: SULFATE OXYGENS ARE NOT VISIBLE IN ELECTRON DENSITY MAP. / 2: RESIDUES PRO 62 AND PRO 71 ARE CIS PROLINES.

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Components

#1: Protein/peptide T CELL SURFACE GLYCOPROTEIN CD4


Mass: 19706.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: OVARY / References: UniProt: P05540
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.35 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
110 mg/mlproteindrop
220 mMTris-HCldrop
358-62 %satammonium sulfatereservoir
420 mMTris-HClreservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 7274 / % possible obs: 99.1 % / Redundancy: 5.7 % / Num. measured all: 41516 / Rmerge(I) obs: 0.065

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→10 Å / Rfactor all: 0.233
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 1 14 1396
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.081
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 7133 / Rfactor obs: 0.233

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