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- PDB-1cdi: STRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS R... -

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Basic information

Entry
Database: PDB / ID: 1cdi
TitleSTRUCTURES OF AN HIV AND MHC BINDING FRAGMENT FROM HUMAN CD4 AS REFINED IN TWO CRYSTAL LATTICES
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 kinase activity / 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 / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of kinase activity / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / regulation of T cell activation / 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 / Co-inhibition by PD-1 / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / T cell activation / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / positive regulation of T cell activation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / MHC class II protein complex binding / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / virus receptor activity / defense response to Gram-negative bacterium / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / early endosome / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / cell adhesion / 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 / Immunoglobulins / 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: 2.9 Å
AuthorsRyu, S.E. / Truneh, A. / Sweet, R.W. / Hendrickson, W.A.
CitationJournal: Structure / Year: 1994
Title: Structures of an HIV and MHC binding fragment from human CD4 as refined in two crystal lattices.
Authors: Ryu, S.E. / Truneh, A. / Sweet, R.W. / Hendrickson, W.A.
History
DepositionJan 26, 1994Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)19,8271
Polymers19,8271
Non-polymers00
Water00
1
A: T CELL SURFACE GLYCOPROTEIN CD4

A: T CELL SURFACE GLYCOPROTEIN CD4


Theoretical massNumber of molelcules
Total (without water)39,6532
Polymers39,6532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Unit cell
Length a, b, c (Å)133.550, 32.270, 46.070
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody T CELL SURFACE GLYCOPROTEIN CD4


Mass: 19826.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01730
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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: referred to 'Ryu, S.-E.', (1990) Nature, 348, 419-426
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-25 %PEG33501reservoir
220 mg/mlprotein1drop
320-25 %PEG33501drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / Num. obs: 3999 / % possible obs: 91 % / Rmerge(I) obs: 0.089

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→10 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.183 -
obs0.183 3235
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 0 0 1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg
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_it0.441
X-RAY DIFFRACTIONx_mcangle_it0.7961.5
X-RAY DIFFRACTIONx_scbond_it0.5451.5
X-RAY DIFFRACTIONx_scangle_it0.912
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / Num. reflection obs: 3235 / σ(F): 4 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.038
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.050.044
X-RAY DIFFRACTIONp_plane_restr0.020.012
X-RAY DIFFRACTIONp_chiral_restr0.150.167
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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