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- PDB-5dfv: CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 5dfv
TitleCRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH MURINE FAB FRAGMENT K04
Components
  • CD81 antigen
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / HELICAL BUNDLE / CELL ADHESION / 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 / 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 / transferrin receptor binding / immunological synapse formation / protein localization to lysosome / tetraspanin-enriched microdomain / positive regulation of T-helper 2 cell cytokine production / positive regulation of protein exit from endoplasmic reticulum / 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 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 / MHC class II protein complex 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
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: 2.8 Å
AuthorsHarris, S.F. / Wong, A. / Kuglstatter, A.
CitationJournal: Mabs / Year: 2016
Title: VH-VL orientation prediction for antibody humanization candidate selection: A case study.
Authors: Bujotzek, A. / Lipsmeier, F. / Harris, S.F. / Benz, J. / Kuglstatter, A. / Georges, G.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
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
C: FAB HEAVY CHAIN
D: FAB LIGHT CHAIN
E: FAB HEAVY CHAIN
F: FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)117,1796
Polymers117,1796
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12660 Å2
ΔGint-87 kcal/mol
Surface area44290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.631, 94.483, 94.114
Angle α, β, γ (deg.)90.00, 104.14, 90.00
Int Tables number4
Space group name H-MP1211

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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: 10947.140 Da / Num. of mol.: 2
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 FAB HEAVY CHAIN


Mass: 23454.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: MURINE HYBRIDOMA
#3: Antibody FAB LIGHT CHAIN


Mass: 24187.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: MURINE HYBRIDOMA
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M NaOAc, 20% PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 30682 / % possible obs: 94 % / Redundancy: 3.4 % / Rsym value: 0.125 / Net I/σ(I): 7.1
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.4 / % possible all: 63.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.25 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.83 / SU B: 17.241 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.442 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29066 1583 5.2 %RANDOM
Rwork0.23947 ---
obs0.24213 29086 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.375 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.64 Å2
2---0.07 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.8→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 0 5 7941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228109
X-RAY DIFFRACTIONr_bond_other_d0.0010.025428
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.9511014
X-RAY DIFFRACTIONr_angle_other_deg0.7853.00313300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08451026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81824.798321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.532151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0231526
X-RAY DIFFRACTIONr_chiral_restr0.0610.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021555
X-RAY DIFFRACTIONr_nbd_refined0.2020.21747
X-RAY DIFFRACTIONr_nbd_other0.1810.25512
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23865
X-RAY DIFFRACTIONr_nbtor_other0.0830.24509
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3651.56596
X-RAY DIFFRACTIONr_mcbond_other0.031.52084
X-RAY DIFFRACTIONr_mcangle_it0.40428336
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.41333530
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6774.52678
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 66 -
Rwork0.364 1250 -
obs--54.83 %

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