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- PDB-3x0g: Crystal structure of the ectodomain of African green monkey CD81 ... -

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Basic information

Entry
Database: PDB / ID: 3x0g
TitleCrystal structure of the ectodomain of African green monkey CD81 large extracellular loop (agmCD81-LEL)
ComponentsCD81
KeywordsCELL ADHESION / disulfide bond / helical bundle / 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 / macrophage fusion / CD4-positive, alpha-beta T cell costimulation / positive regulation of B cell receptor signaling pathway / osteoclast fusion / myoblast fusion involved in skeletal muscle regeneration / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of inflammatory response to antigenic stimulus / regulation of macrophage migration ...positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / macrophage fusion / CD4-positive, alpha-beta T cell costimulation / positive regulation of B cell receptor signaling pathway / osteoclast fusion / myoblast fusion involved in skeletal muscle regeneration / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of inflammatory response to antigenic stimulus / regulation of macrophage migration / immunological synapse formation / transferrin receptor binding / tetraspanin-enriched microdomain / positive regulation of protein exit from endoplasmic reticulum / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / humoral immune response mediated by circulating immunoglobulin / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / cholesterol binding / positive regulation of T cell receptor signaling pathway / immunological synapse / cellular response to low-density lipoprotein particle stimulus / positive regulation of receptor clustering / positive regulation of B cell proliferation / protein localization to plasma membrane / regulation of protein stability / receptor internalization / integrin binding / virus receptor activity / basolateral plasma membrane / positive regulation of MAPK cascade / positive regulation of transcription by RNA polymerase II / extracellular exosome / cytosol
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 speciesChlorocebus sabaeus (green monkey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 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 / 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_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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: CD81
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5594
Polymers10,2051
Non-polymers3553
Water1,00956
1
A: CD81
hetero molecules

A: CD81
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1188
Polymers20,4092
Non-polymers7096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3620 Å2
ΔGint-94 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.156, 39.700, 59.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein CD81


Mass: 10204.521 Da / Num. of mol.: 1 / Fragment: large extracellular loop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorocebus sabaeus (green monkey) / Gene: CD81 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A0D9RBI8*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% Ethanol, 5% MPD, 0.1M Tris pH 8.5, 200mM Sodium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2014 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.899→27.878 Å / Num. all: 7800 / Num. obs: 7580 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.93 % / Biso Wilson estimate: 31.196 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.28
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.42 / Num. unique all: 1219 / % possible all: 83.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BKH

4bkh
PDB Unreleased entry


Resolution: 1.899→25.276 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 347 4.59 %RANDOM
Rwork0.2309 ---
obs0.232 7565 97.12 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.585 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 30.81 Å2
Baniso -1Baniso -2Baniso -3
1--5.0533 Å20 Å20 Å2
2--0.8344 Å20 Å2
3---4.2189 Å2
Refinement stepCycle: LAST / Resolution: 1.899→25.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms712 0 24 56 792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009751
X-RAY DIFFRACTIONf_angle_d1.1631012
X-RAY DIFFRACTIONf_dihedral_angle_d17.478270
X-RAY DIFFRACTIONf_chiral_restr0.065120
X-RAY DIFFRACTIONf_plane_restr0.004127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8995-2.39280.27111570.2419344094
2.3928-25.2780.24851900.22713778100

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