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- PDB-6ek2: CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 6ek2
TitleCRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH SINGLE CHAIN FV FRAGMENT 10
Components
  • CD81 antigen
  • SINGLE CHAIN FV FRAGMENT
KeywordsCELL ADHESION / HELICAL BUNDLE / ANTIBODY-ANTIGEN COMPLEX
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 / protein localization to lysosome / tetraspanin-enriched microdomain / positive regulation of protein exit from endoplasmic reticulum / positive regulation of T-helper 2 cell cytokine production / 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 / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of receptor clustering / positive regulation of B cell proliferation / Regulation of Complement cascade / basal plasma membrane / protein localization to plasma membrane / regulation of protein stability / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / integrin binding / virus receptor activity / basolateral plasma membrane / vesicle / positive regulation of MAPK cascade / focal adhesion / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane / 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 / Immunoglobulins / Immunoglobulin-like ...Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHarris, S.F. / Villasenor, A. / Kuglstatter, A.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structure-Guided Combinatorial Engineering Facilitates Affinity and Specificity Optimization of Anti-CD81 Antibodies.
Authors: Nelson, B. / Adams, J. / Kuglstatter, A. / Li, Z. / Harris, S.F. / Liu, Y. / Bohini, S. / Ma, H. / Klumpp, K. / Gao, J. / Sidhu, S.S.
History
DepositionSep 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
H: SINGLE CHAIN FV FRAGMENT
I: SINGLE CHAIN FV FRAGMENT


Theoretical massNumber of molelcules
Total (without water)74,3504
Polymers74,3504
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-26 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.317, 118.060, 130.130
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 / Tetraspanin-28 / Tspan-28


Mass: 10808.992 Da / Num. of mol.: 2 / Fragment: UNP residues 112-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Production host: Escherichia coli (E. coli) / References: UniProt: P60033
#2: Antibody SINGLE CHAIN FV FRAGMENT


Mass: 26366.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1 M Bis-Tris, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.65→43.72 Å / Num. obs: 17696 / % possible obs: 72.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 47.28 Å2 / Rsym value: 0.177 / Net I/σ(I): 8
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 2 / Num. unique obs: 141 / Rsym value: 0.335 / % possible all: 5.9

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→43.72 Å / Cor.coef. Fo:Fc: 0.9274 / Cor.coef. Fo:Fc free: 0.8851 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 933 5.29 %RANDOM
Rwork0.1786 ---
obs0.1822 17650 72.6 %-
Displacement parametersBiso mean: 46.01 Å2
Baniso -1Baniso -2Baniso -3
1-6.2004 Å20 Å20 Å2
2---8.4249 Å20 Å2
3---2.2246 Å2
Refine analyzeLuzzati coordinate error obs: 0.322 Å
Refinement stepCycle: 1 / Resolution: 2.65→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4905 0 0 257 5162
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095016HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.246788HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1708SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes723HARMONIC5
X-RAY DIFFRACTIONt_it5016HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion22.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion654SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5797SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.81 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2771 26 6.67 %
Rwork0.228 364 -
all0.2318 390 -

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