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- PDB-5x0t: Crystal structure of CD147 C2 domain in complex with Fab of its m... -

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Basic information

Entry
Database: PDB / ID: 5x0t
TitleCrystal structure of CD147 C2 domain in complex with Fab of its monoclonal antibody 6H8
Components
  • 6H8 Fab fragment heavy chain
  • 6H8 Fab fragment light chain
  • Basigin
KeywordsIMMUNE SYSTEM / CD147 / monoclonal antibody
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / neural retina development / endothelial tube morphogenesis / Pyruvate metabolism / photoreceptor cell maintenance / Basigin interactions ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / neural retina development / endothelial tube morphogenesis / Pyruvate metabolism / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / mannose binding / decidualization / photoreceptor outer segment / positive regulation of vascular endothelial growth factor production / Integrin cell surface interactions / embryo implantation / response to cAMP / photoreceptor inner segment / Degradation of the extracellular matrix / neutrophil chemotaxis / positive regulation of endothelial cell migration / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / virus receptor activity / signaling receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLin, P. / Zhang, M.-Y. / Ye, S. / Chen, X. / Yu, X.-L. / Zhang, R.-G. / Zhu, P. / Chen, Z.-N.
Funding support China, 2items
OrganizationGrant numberCountry
National Science and Technology Major Projects2013ZX09301301 China
National Basic Research Project(973 Program)2015CB553701 China
CitationJournal: To Be Published
Title: Crystal structure of CD147 C2 domain in complex with Fab of its monoclonal antibody
Authors: Zhang, M.-Y. / Lin, P. / Zhu, P. / Chen, Z.-N.
History
DepositionJan 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6H8 Fab fragment heavy chain
C: 6H8 Fab fragment heavy chain
B: 6H8 Fab fragment light chain
D: 6H8 Fab fragment light chain
E: Basigin
F: Basigin


Theoretical massNumber of molelcules
Total (without water)124,1716
Polymers124,1716
Non-polymers00
Water3,405189
1
A: 6H8 Fab fragment heavy chain
B: 6H8 Fab fragment light chain
E: Basigin


Theoretical massNumber of molelcules
Total (without water)62,0853
Polymers62,0853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 6H8 Fab fragment heavy chain
D: 6H8 Fab fragment light chain
F: Basigin


Theoretical massNumber of molelcules
Total (without water)62,0853
Polymers62,0853
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.986, 83.486, 130.193
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 6H8 Fab fragment heavy chain


Mass: 26331.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody 6H8 Fab fragment light chain


Mass: 25913.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein Basigin / / CD147


Mass: 9840.018 Da / Num. of mol.: 2 / Fragment: C2 domain, UNP residues 22-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BSG, UNQ6505/PRO21383 / Production host: Escherichia coli (E. coli) / References: UniProt: P35613
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.2M lithium sulfate monohydrate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→43.34 Å / Num. obs: 33828 / % possible obs: 97 % / Redundancy: 1 % / Net I/σ(I): 20.1
Reflection shellResolution: 2.5→2.62 Å / Redundancy: 1 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 7.1 / % possible all: 84.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.5→37.161 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2999 1688 4.99 %
Rwork0.2458 --
obs0.2485 33808 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→37.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7792 0 0 189 7981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057986
X-RAY DIFFRACTIONf_angle_d0.91910876
X-RAY DIFFRACTIONf_dihedral_angle_d15.6374764
X-RAY DIFFRACTIONf_chiral_restr0.0561224
X-RAY DIFFRACTIONf_plane_restr0.0051382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57360.36451380.28112273X-RAY DIFFRACTION83
2.5736-2.65660.37491160.2752418X-RAY DIFFRACTION88
2.6566-2.75150.34741450.26592660X-RAY DIFFRACTION96
2.7515-2.86170.3551280.26752714X-RAY DIFFRACTION99
2.8617-2.99190.30691450.27352770X-RAY DIFFRACTION100
2.9919-3.14950.35611490.27582735X-RAY DIFFRACTION99
3.1495-3.34670.36151450.2552758X-RAY DIFFRACTION100
3.3467-3.60490.29991330.25142749X-RAY DIFFRACTION99
3.6049-3.96730.28381300.24142752X-RAY DIFFRACTION99
3.9673-4.54060.26411500.21972745X-RAY DIFFRACTION99
4.5406-5.71730.2351360.21082779X-RAY DIFFRACTION99
5.7173-37.16560.25241730.22812767X-RAY DIFFRACTION98

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