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

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Basic information

Entry
Database: PDB / ID: 5dfw
TitleCRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH SINGLE CHAIN FV FRAGMENT K13
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 / 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 / immunological synapse formation / transferrin receptor binding / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / tetraspanin-enriched microdomain / 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 / 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 / protein localization to plasma membrane / Regulation of Complement cascade / regulation of protein stability / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / virus receptor activity / MHC class II protein complex binding / 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: 2.33 Å
AuthorsHarris, S.F. / Villasenor, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD81 antigen
H: SINGLE CHAIN FV FRAGMENT


Theoretical massNumber of molelcules
Total (without water)36,6592
Polymers36,6592
Non-polymers00
Water1,49583
1
A: CD81 antigen
H: SINGLE CHAIN FV FRAGMENT

A: CD81 antigen
H: SINGLE CHAIN FV FRAGMENT


Theoretical massNumber of molelcules
Total (without water)73,3174
Polymers73,3174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4440 Å2
ΔGint-22 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.652, 49.671, 80.452
Angle α, β, γ (deg.)90.00, 105.30, 90.00
Int Tables number3
Space group name H-MP121

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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.: 1 / 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: 25849.518 Da / Num. of mol.: 1 / Fragment: UNP Residues 101-810
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 / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% peg 3350, 0.2 M sodium formate, 0.1 M sodium citrate

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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: Jul 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 11229 / % possible obs: 68.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 30.59 Å2 / Rsym value: 0.083 / Net I/σ(I): 12.8
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 2.2 / % possible all: 17.9

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Processing

Software
NameVersionClassification
BUSTER2.9.2refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→41.83 Å / Cor.coef. Fo:Fc: 0.9124 / Cor.coef. Fo:Fc free: 0.864 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 577 5.14 %RANDOM
Rwork0.1902 ---
obs0.1938 11218 68.2 %-
Displacement parametersBiso mean: 46.48 Å2
Baniso -1Baniso -2Baniso -3
1-6.4868 Å20 Å211.6174 Å2
2---9.4772 Å20 Å2
3---2.9904 Å2
Refine analyzeLuzzati coordinate error obs: 0.312 Å
Refinement stepCycle: 1 / Resolution: 2.33→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 0 83 2501
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012477HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.223366HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d825SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes358HARMONIC5
X-RAY DIFFRACTIONt_it2477HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion23.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion330SEMIHARMONIC5
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_contact2865SEMIHARMONIC4
LS refinement shellResolution: 2.33→2.55 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 48 5.2 %
Rwork0.2423 875 -
all0.2458 923 -

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