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- PDB-7xy8: Crystal structure of antibody Fab fragment in complex with CD147(... -

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Basic information

Entry
Database: PDB / ID: 7xy8
TitleCrystal structure of antibody Fab fragment in complex with CD147(EMMPIRIN)
Components
  • Isoform 2 of Basigin
  • heavy chain
  • light chain
KeywordsPROTEIN BINDING / cd147 / complex / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNakamura, K. / Amano, M. / Yoneda, K. / Suzuki, M. / Fukuchi, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Oncol / Year: 2022
Title: Novel Antibody Exerts Antitumor Effect through Downregulation of CD147 and Activation of Multiple Stress Signals
Authors: Qin, S. / Fukuchi, K. / Nanai, K. / Yuita, H. / Maru, C. / Tsukada, J. / Ishigami, M. / Nagai, Y. / Nakano, Y. / Yoshimura, C. / Yoneda, K. / Amano, M. / Nakamura, K. / Oda, Y. / Nishigohri, ...Authors: Qin, S. / Fukuchi, K. / Nanai, K. / Yuita, H. / Maru, C. / Tsukada, J. / Ishigami, M. / Nagai, Y. / Nakano, Y. / Yoshimura, C. / Yoneda, K. / Amano, M. / Nakamura, K. / Oda, Y. / Nishigohri, H. / Yamamoto, S. / Ohnishi-Totoki, Y. / Inaki, K. / Komori, H. / Nakano, R. / Kanari, Y. / Nishida, A. / Matsui, Y. / Funo, S. / Takahashi, S. / Ohtsuka, T. / Agatsuma, T.
History
DepositionJun 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Basigin
B: Isoform 2 of Basigin
H: heavy chain
I: heavy chain
L: light chain
M: light chain


Theoretical massNumber of molelcules
Total (without water)142,4286
Polymers142,4286
Non-polymers00
Water3,369187
1
A: Isoform 2 of Basigin
H: heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)71,2143
Polymers71,2143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2 of Basigin
I: heavy chain
M: light chain


Theoretical massNumber of molelcules
Total (without water)71,2143
Polymers71,2143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.960, 93.370, 98.309
Angle α, β, γ (deg.)90.000, 90.890, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12H
22I
13L
23M

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARGAA103 - 201103 - 201
21GLYGLYARGARGBB103 - 201103 - 201
12GLNGLNLYSLYSHC1 - 2181 - 218
22GLNGLNLYSLYSID1 - 2181 - 218
13ASPASPCYSCYSLE1 - 2141 - 214
23ASPASPCYSCYSMF1 - 2141 - 214

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Isoform 2 of Basigin / 5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / ...5F7 / Collagenase stimulatory factor / Extracellular matrix metalloproteinase inducer / EMMPRIN / Hepatoma-associated antigen / HAb18G / Leukocyte activation antigen M6 / OK blood group antigen / Tumor cell-derived collagenase stimulatory factor / TCSF


Mass: 22503.928 Da / Num. of mol.: 2
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: Antibody heavy chain


Mass: 25277.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#3: Antibody light chain /


Mass: 23432.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M Sodium Malonate pH 7.0, 12% (w/v) Polyethylene Glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen gas flow (95K-300K) / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2018
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→35.911 Å / Num. obs: 51301 / % possible obs: 98.4 % / Redundancy: 3 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.105 / Rsym value: 0.086 / Net I/av σ(I): 5.4 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7430 / Rpim(I) all: 0.247 / Rrim(I) all: 0.439 / Rsym value: 0.36 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3b5h

3b5h


Resolution: 2.3→35.91 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.455 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 2502 4.9 %RANDOM
Rwork0.2358 ---
obs0.238 48775 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.51 Å2 / Biso mean: 43.373 Å2 / Biso min: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å2-0 Å2-0.66 Å2
2---0.06 Å2-0 Å2
3----2.28 Å2
Refinement stepCycle: final / Resolution: 2.3→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8702 0 0 187 8889
Biso mean---31.84 -
Num. residues----1139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198903
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.94412079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38651132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88724.411365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.723151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8031543
X-RAY DIFFRACTIONr_chiral_restr0.0840.21348
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216648
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1940.12
12B1940.12
21H5180.12
22I5180.12
31L5400.14
32M5400.14
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 142 -
Rwork0.314 3576 -
all-3718 -
obs--97.43 %

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