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- PDB-3qqn: The retinal specific CD147 Ig0 domain: from molecular structure t... -

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Basic information

Entry
Database: PDB / ID: 3qqn
TitleThe retinal specific CD147 Ig0 domain: from molecular structure to biological activity
ComponentsBasigin
KeywordsCELL ADHESION / CD147 / EMMPRIN / Immunoglobulin-like domain / beta sheet / Structural Genomics / Berkeley Structural Genomics Center / BSGC
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 / D-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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.309 Å
AuthorsRedzic, J.S. / Armstrong, G.S. / Isern, N.G. / Kieft, J.S. / Eisenmesser, E.Z. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Retinal Specific CD147 Ig0 Domain: From Molecular Structure to Biological Activity.
Authors: Redzic, J.S. / Armstrong, G.S. / Isern, N.G. / Jones, D.N. / Kieft, J.S. / Eisenmesser, E.Z.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basigin
B: Basigin


Theoretical massNumber of molelcules
Total (without water)30,9392
Polymers30,9392
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.240, 80.240, 160.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:96 or resseq 103:117 )
211chain B and (resseq 2:96 or resseq 103:117 )

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Components

#1: Antibody Basigin / / 5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / ...5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / Leukocyte activation antigen M6 / OK blood group antigen / Tumor cell-derived collagenase stimulatory factor / TCSF


Mass: 15469.710 Da / Num. of mol.: 2 / Fragment: UNP residues 23-138 / Mutation: C46M
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAS PER AUTHORS ILE IS THE CORRECT RESIDUE AT POSITION 45

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Ammonium Sulfate, 20% PEG 3350, 0.1M spermidine tetrachloride, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.02159,1.02195,1.03726
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 28, 2009
RadiationMonochromator: Rosenbaum-Rock double Si111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.021591
21.021951
31.037261
ReflectionResolution: 2.309→42.42 Å / Num. obs: 14020 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine:1.5_2)model building
PHENIX(phenix.refine: 1.5_2)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementResolution: 2.309→42.42 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 25.77 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2686 1395 10 %
Rwork0.2345 --
obs0.238 13954 98.82 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.302 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2544 Å20 Å2-0 Å2
2---2.2544 Å20 Å2
3---4.5089 Å2
Refinement stepCycle: LAST / Resolution: 2.309→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 0 158 1994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091888
X-RAY DIFFRACTIONf_angle_d1.3532578
X-RAY DIFFRACTIONf_dihedral_angle_d17.033664
X-RAY DIFFRACTIONf_chiral_restr0.099278
X-RAY DIFFRACTIONf_plane_restr0.007340
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A870X-RAY DIFFRACTIONPOSITIONAL
12B870X-RAY DIFFRACTIONPOSITIONAL0.069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.309-2.39120.33521210.28951099X-RAY DIFFRACTION89
2.3912-2.48690.32831390.25711230X-RAY DIFFRACTION100
2.4869-2.60010.29141370.26381236X-RAY DIFFRACTION100
2.6001-2.73710.29021360.23551238X-RAY DIFFRACTION100
2.7371-2.90860.26141420.24191250X-RAY DIFFRACTION100
2.9086-3.13310.27191370.24681256X-RAY DIFFRACTION100
3.1331-3.44820.30181390.24111255X-RAY DIFFRACTION100
3.4482-3.94690.26241430.24351276X-RAY DIFFRACTION100
3.9469-4.97140.20471430.18671316X-RAY DIFFRACTION100
4.9714-42.420.28681580.24441403X-RAY DIFFRACTION100

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