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- PDB-7mws: Crystal structure of tamarin CD81 large extracellular loop -

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Basic information

Entry
Database: PDB / ID: 7mws
TitleCrystal structure of tamarin CD81 large extracellular loop
ComponentsCD81 protein
KeywordsSTRUCTURAL PROTEIN / Receptor protein / PROTEIN BINDING
Function / homology
Function and homology information


: / 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 ...: / 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 / positive regulation of T-helper 2 cell cytokine production / tetraspanin-enriched microdomain / positive regulation of B cell activation / positive regulation of protein exit from endoplasmic reticulum / humoral immune response mediated by circulating immunoglobulin / positive regulation of CD4-positive, alpha-beta T cell proliferation / cholesterol binding / positive regulation of T cell receptor signaling pathway / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of receptor clustering / protein localization to plasma membrane / protein localization / receptor internalization / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / basolateral plasma membrane / positive regulation of MAPK cascade / positive regulation of cell population proliferation / membrane / plasma membrane
Similarity search - Function
Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family
Similarity search - Domain/homology
Biological speciesSaguinus oedipus (cotton-top tamarin)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKumar, A. / Hossain, R.A. / Yost, S.A. / Bu, W. / Wang, Y. / Dearborn, A.D. / Grakoui, A. / Cohen, J.I. / Marcotrigiano, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nature / Year: 2021
Title: Structural insights into hepatitis C virus receptor binding and entry.
Authors: Kumar, A. / Hossain, R.A. / Yost, S.A. / Bu, W. / Wang, Y. / Dearborn, A.D. / Grakoui, A. / Cohen, J.I. / Marcotrigiano, J.
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
A: CD81 protein
B: CD81 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4645
Polymers20,9842
Non-polymers4813
Water1,18966
1
A: CD81 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6862
Polymers10,4921
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CD81 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7783
Polymers10,4921
Non-polymers2862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.263, 113.263, 113.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein CD81 protein


Mass: 10491.831 Da / Num. of mol.: 2 / Fragment: second extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saguinus oedipus (cotton-top tamarin) / Cell line: HEK293T GnTI- cells / Gene: CD81 / Cell line (production host): HEK293T GnTI- cells / Production host: Homo sapiens (human) / Strain (production host): 9606 / References: UniProt: Q9N0J9
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, and 55% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→40.04 Å / Num. obs: 22547 / % possible obs: 100 % / Redundancy: 40.1 % / CC1/2: 0.99 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.87 Å / Num. unique obs: 1651 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALAdata scaling
Coot0.8.9.2 ELmodel building
DIALS7.0.077data collection
MOSFLM7.2.2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8Q

1g8q


Resolution: 1.8→40.04 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 1186 5.27 %
Rwork0.207 --
obs0.2083 22509 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 32 66 1513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141474
X-RAY DIFFRACTIONf_angle_d1.3791987
X-RAY DIFFRACTIONf_dihedral_angle_d5.5421052
X-RAY DIFFRACTIONf_chiral_restr0.069236
X-RAY DIFFRACTIONf_plane_restr0.008256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88180.31261740.28762619X-RAY DIFFRACTION100
1.8818-1.9810.25611600.25242615X-RAY DIFFRACTION100
1.981-2.10510.23661600.21852624X-RAY DIFFRACTION100
2.1051-2.26760.27441160.20222693X-RAY DIFFRACTION100
2.2676-2.49580.22821610.19882631X-RAY DIFFRACTION100
2.4958-2.85690.22251530.19092673X-RAY DIFFRACTION100
2.8569-3.5990.22971060.2142712X-RAY DIFFRACTION100
3.599-400.22481560.20292756X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 24.1892 Å / Origin y: 42.1044 Å / Origin z: 3.7853 Å
111213212223313233
T0.2045 Å20.0573 Å20.0635 Å2-0.3352 Å20.0243 Å2--0.2475 Å2
L4.3461 °2-0.6488 °23.3478 °2-2.3775 °2-1.0494 °2--6.0486 °2
S0.0404 Å °-0.5268 Å °0.0222 Å °-0.0211 Å °-0.1089 Å °0.026 Å °0.2043 Å °-0.4456 Å °0.0262 Å °
Refinement TLS groupSelection details: all

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