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

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Basic information

Entry
Database: PDB / ID: 6ejg
TitleCRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH SINGLE CHAIN FV FRAGMENT 4
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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsHarris, S.F. / Wong, 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 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD81 antigen
B: CD81 antigen
C: SINGLE CHAIN FV FRAGMENT
D: SINGLE CHAIN FV FRAGMENT


Theoretical massNumber of molelcules
Total (without water)74,6434
Polymers74,6434
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-29 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.635, 170.905, 185.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 10922.150 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 SINGLE CHAIN FV FRAGMENT


Mass: 26399.332 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.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 4.19 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 mM sodium citrate, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.82→46.83 Å / Num. obs: 27051 / % possible obs: 88.3 % / Redundancy: 6.3 % / Rsym value: 0.17 / Net I/σ(I): 9.7
Reflection shellResolution: 2.82→2.92 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1126 / Rsym value: 0.494 / % possible all: 37.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→46.83 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.873 / SU B: 12.326 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.63 / ESU R Free: 0.346 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26272 1348 5 %RANDOM
Rwork0.22702 ---
obs0.22874 25664 88.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.385 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.49 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.82→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 0 57 4959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0225022
X-RAY DIFFRACTIONr_bond_other_d0.0010.023396
X-RAY DIFFRACTIONr_angle_refined_deg0.991.9516794
X-RAY DIFFRACTIONr_angle_other_deg0.763.0038308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85524.951206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93915860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9391516
X-RAY DIFFRACTIONr_chiral_restr0.0590.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02984
X-RAY DIFFRACTIONr_nbd_refined0.1870.21009
X-RAY DIFFRACTIONr_nbd_other0.1760.23409
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22397
X-RAY DIFFRACTIONr_nbtor_other0.0830.22729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1450.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3121.54102
X-RAY DIFFRACTIONr_mcbond_other0.0241.51310
X-RAY DIFFRACTIONr_mcangle_it0.34125102
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.35432219
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5894.51692
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: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 39 -
Rwork0.336 686 -
obs--32.64 %

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