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- PDB-1iv5: New Crystal Form of Human CD81 Large Extracellular Loop. -

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Basic information

Entry
Database: PDB / ID: 1iv5
TitleNew Crystal Form of Human CD81 Large Extracellular Loop.
ComponentsCD81 antigen
KeywordsIMMUNE SYSTEM / Alpha domain / Five Helix
Function / homology
Function and homology information


positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion ...positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion / immunological synapse formation / tetraspanin-enriched microdomain / transferrin receptor binding / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / positive regulation of protein exit from endoplasmic reticulum / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / humoral immune response mediated by circulating immunoglobulin / cholesterol binding / positive regulation of T cell receptor signaling pathway / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of B cell proliferation / positive regulation of receptor clustering / basal plasma membrane / Regulation of Complement cascade / protein localization to plasma membrane / regulation of protein stability / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / virus receptor activity / MHC class II protein complex binding / basolateral plasma membrane / vesicle / positive regulation of MAPK cascade / focal adhesion / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKitadokoro, K. / Bolognesi, M. / Grandi, G. / Marco, P. / Galli, G. / Petracca, R. / Fabiana, F.
CitationJournal: Biol.Chem. / Year: 2002
Title: Subunit Association and Conformational Flexibility in the Head-subdomain of Human CD81 Large Extracellular Loop.
Authors: Kitadokoro, K. / Ponassi, M. / Galli, G. / Petracca, R. / Falugi, F. / Grandi, G. / Bolognesi, M.
History
DepositionMar 14, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: CD81 antigen
B: CD81 antigen


Theoretical massNumber of molelcules
Total (without water)19,8342
Polymers19,8342
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-17 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.052, 102.052, 35.283
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsThe second part of the biological assembly is generated by the two fold axis.

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Components

#1: Protein CD81 antigen / 26 kDa cell surface protein TAPA-1


Mass: 9917.077 Da / Num. of mol.: 2 / Fragment: CD81 large extracellular loop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEZZ 18 / Production host: Escherichia coli (E. coli) / References: UniProt: P60033
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 4000, DMSO, sodium chloride, sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 31746 / Num. obs: 32025 / % possible obs: 98.2 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.206 / Num. unique all: 597 / % possible all: 89

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMAC5refinement
RefinementResolution: 2.6→18.73 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.851 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 1.285 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 646 9.9 %RANDOM
Rwork0.2287 ---
all0.23376 6521 --
obs0.23376 6648 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.481 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-
2---0.01 Å2-
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→18.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 0 15 1403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211393
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.941878
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4713174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.73315251
X-RAY DIFFRACTIONr_chiral_restr0.1560.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3410.3791
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.5103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4190.321
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7870.51
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it4.3041888
X-RAY DIFFRACTIONr_mcangle_it7.73621424
X-RAY DIFFRACTIONr_scbond_it11.2193505
X-RAY DIFFRACTIONr_scangle_it13.3423454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 35 -
Rwork0.298 360 -
obs--98.09 %

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