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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 / Co-inhibition by PD-1 / Downstream TCR signaling / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / cellular response to ionomycin / Alpha-defensins / response to methamphetamine hydrochloride / Other interleukin signaling / helper T cell enhancement of adaptive immune response ...Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Downstream TCR signaling / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / cellular response to ionomycin / Alpha-defensins / response to methamphetamine hydrochloride / Other interleukin signaling / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / response to vitamin D / positive regulation of monocyte differentiation / regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of calcium ion transport into cytosol / immunoglobulin binding / macrophage differentiation / regulation of calcium ion transport / T cell differentiation / positive regulation of T cell proliferation / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / protein tyrosine kinase binding / calcium-mediated signaling / positive regulation of T cell activation / MHC class II protein complex binding / response to estradiol / defense response to Gram-negative bacterium / adaptive immune response / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / cell adhesion / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / lipid binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / cell surface / 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 V-Type ...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 V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD4
Similarity search - Component
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.
History
DepositionJan 28, 1993Processing site: BNL
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
Revision 2.0Jun 5, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 2.1Nov 20, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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.
Components on special symmetry positions
IDModelComponents
11A-232-

HOH

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Components

#1: Protein 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
#3: Water ChemComp-HOH / water


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

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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
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMTris-HCl1drop
358-62 %satammonium sulfate1reservoir
420 mMTris-HCl1reservoir

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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
Refine-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
Solvent computation
*PLUS
Displacement parameters
*PLUS

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