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- PDB-3x0f: Crystal structure of the ectodomain of mouse CD81 large extracell... -

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Basic information

Entry
Database: PDB / ID: 3x0f
TitleCrystal structure of the ectodomain of mouse CD81 large extracellular loop (mCD81-LEL)
ComponentsCD81 antigen
KeywordsCELL ADHESION / helical bundle / disulfide bond / immune cell adhesion / morphology / activation / proliferation / differentiation / Membrane
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 ...: / 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 Complement cascade / regulation of macrophage migration / macrophage fusion / transferrin receptor binding / immunological synapse formation / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / tetraspanin-enriched microdomain / positive regulation of B cell activation / positive regulation of protein exit from endoplasmic reticulum / MHC class II protein binding / humoral immune response mediated by circulating immunoglobulin / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of cell motility / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cholesterol binding / positive regulation of T cell receptor signaling pathway / plasma membrane => GO:0005886 / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of B cell proliferation / positive regulation of receptor clustering / basal plasma membrane / protein localization to plasma membrane / regulation of protein stability / protein localization / receptor internalization / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / virus receptor activity / regulation of cell population proliferation / positive regulation of cell growth / basolateral plasma membrane / vesicle / membrane => GO:0016020 / apical plasma membrane / positive regulation of cell population proliferation / 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
ISOPROPYL ALCOHOL / CD81 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.471 Å
AuthorsZhang, M. / Cui, S.
CitationJournal: Faseb J. / Year: 2015
Title: An intramolecular bond at cluster of differentiation 81 ectodomain is important for hepatitis C virus entry.
Authors: Yang, W. / Zhang, M. / Chi, X. / Liu, X. / Qin, B. / Cui, S.
History
DepositionOct 14, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8026
Polymers20,5612
Non-polymers2404
Water1,53185
1
A: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4614
Polymers10,2811
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3412
Polymers10,2811
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.617, 57.922, 62.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CD81 antigen / 26 kDa cell surface protein TAPA-1 / Target of the antiproliferative antibody 1


Mass: 10280.641 Da / Num. of mol.: 2 / Fragment: large extracellular loop, UNP residues 113-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd81, Tapa1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P35762
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.95 Å3/Da / Density % sol: 36.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Sodium Citrate pH 5.5, 5% PEG 1000, 35% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2014 / Details: mirrors
RadiationMonochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.471→44.617 Å / Num. all: 52822 / Num. obs: 52310 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 31.568 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 22.63
Reflection shellResolution: 1.47→1.56 Å / Redundancy: 3.18 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.09 / Num. unique all: 8532 / % possible all: 97.8

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8Q

1g8q


Resolution: 1.471→36.231 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.19 / Phase error: 23.64 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 1397 5.01 %RANDOM
Rwork0.1972 ---
obs0.1997 27883 99.65 %-
all-52822 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.02 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso mean: 43.626 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å20 Å2
2--0.4137 Å20 Å2
3---1.3963 Å2
Refinement stepCycle: LAST / Resolution: 1.471→36.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 16 85 1440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021419
X-RAY DIFFRACTIONf_angle_d0.6291926
X-RAY DIFFRACTIONf_dihedral_angle_d11.715527
X-RAY DIFFRACTIONf_chiral_restr0.034232
X-RAY DIFFRACTIONf_plane_restr0.003254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4711-1.52370.32631350.2601256098
1.5237-1.58470.29931360.24092596100
1.5847-1.65680.29461390.19732630100
1.6568-1.74420.30761380.2072614100
1.7442-1.85340.24151370.18642617100
1.8534-1.99650.28231400.17382647100
1.9965-2.19740.22071400.16242648100
2.1974-2.51530.23881410.16232674100
2.5153-3.16880.22371420.18152693100
3.1688-36.24150.23991490.2218280799

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