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- PDB-1hnf: CRYSTAL STRUCTURE OF THE EXTRACELLULAR REGION OF THE HUMAN CELL A... -

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Basic information

Entry
Database: PDB / ID: 1hnf
TitleCRYSTAL STRUCTURE OF THE EXTRACELLULAR REGION OF THE HUMAN CELL ADHESION MOLECULE CD2 AT 2.5 ANGSTROMS RESOLUTION
ComponentsCD2
KeywordsT LYMPHOCYTE ADHESION GLYCOPROTEIN
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / T cell activation / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cell-cell adhesion ...positive regulation of myeloid dendritic cell activation / membrane raft polarization / natural killer cell activation / heterotypic cell-cell adhesion / regulation of T cell differentiation / natural killer cell mediated cytotoxicity / T cell activation / positive regulation of interleukin-8 production / Cell surface interactions at the vascular wall / cell-cell adhesion / receptor tyrosine kinase binding / cytoplasmic side of plasma membrane / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cell-cell junction / signaling receptor activity / cell surface receptor signaling pathway / immune response / external side of plasma membrane / signaling receptor binding / apoptotic process / cell surface / Golgi apparatus / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface antigen CD2 / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...T-cell surface antigen CD2 / : / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface antigen CD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBodian, D.L. / Jones, E.Y. / Harlos, K. / Stuart, D.I. / Davis, S.J.
Citation
Journal: Structure / Year: 1994
Title: Crystal structure of the extracellular region of the human cell adhesion molecule CD2 at 2.5 A resolution.
Authors: Bodian, D.L. / Jones, E.Y. / Harlos, K. / Stuart, D.I. / Davis, S.J.
#1: Journal: To be Published
Title: Ligand Binding by the Immunoglobulin Superfamily Recognition Molecule Cd2 is Glycosylation Independent
Authors: Davis, S.J. / Davies, E.A. / Barclay, A.N. / Daenke, S. / Bodian, D.L. / Jones, E.Y. / Stuart, D.I. / Butters, T.D. / Dwek, R.A. / Van Der Merwe, P.A.
#2: Journal: Nature / Year: 1992
Title: Crystal Structure at 2.8 Angstroms Resolution of a Soluble Form of the Cell Adhesion Molecule Cd2
Authors: Jones, E.Y. / Davis, S.J. / Williams, A.F. / Harlos, K. / Stuart, D.I.
History
DepositionAug 10, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6895
Polymers21,0021
Non-polymers6874
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.300, 88.300, 51.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: THE IDENTITY OF THE NA 629 ION HAS NOT BEEN CONFIRMED.

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Components

#1: Protein CD2


Mass: 21002.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: OVARY / References: UniProt: P06729
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE AUTHOR STATES THAT THE IDENTITY OF THE NA 629 ION HAS NOT BEEN CONFIRMED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.25 MNa citrate1reservoir
20.1 MNa HEPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 7181 / % possible obs: 87 %
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 27413 / Rmerge(I) obs: 0.045

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→24 Å /
RfactorNum. reflection
Rwork0.193 -
obs0.193 7181
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 43 22 1512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
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_deg1.97
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: 0.193 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_d1.97

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