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- PDB-6lyn: CD146 D4-D5/AA98 Fab -

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Basic information

Entry
Database: PDB / ID: 6lyn
TitleCD146 D4-D5/AA98 Fab
Components
  • AA98 Fab heavy chain
  • AA98 Fab light chain
  • Cell surface glycoprotein MUC18
KeywordsCELL ADHESION / CD146 / AA98
Function / homology
Function and homology information


glomerular filtration / vascular wound healing / anatomical structure morphogenesis / angiogenesis / membrane => GO:0016020 / cell adhesion / positive regulation of cell migration / external side of plasma membrane / focal adhesion / extracellular space ...glomerular filtration / vascular wound healing / anatomical structure morphogenesis / angiogenesis / membrane => GO:0016020 / cell adhesion / positive regulation of cell migration / external side of plasma membrane / focal adhesion / extracellular space / extracellular region / nucleus / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / Cell surface glycoprotein MUC18
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.776 Å
AuthorsChen, X. / Yan, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770793 China
National Natural Science Foundation of China (NSFC)31370740 China
CitationJournal: Iscience / Year: 2021
Title: Structure basis for AA98 inhibition on the activation of endothelial cells mediated by CD146.
Authors: Chen, X. / Yan, H. / Liu, D. / Xu, Q. / Duan, H. / Feng, J. / Yan, X. / Xie, C.
History
DepositionFeb 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AA98 Fab heavy chain
B: AA98 Fab light chain
C: Cell surface glycoprotein MUC18
L: AA98 Fab light chain
D: Cell surface glycoprotein MUC18
H: AA98 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,61321
Polymers135,6446
Non-polymers1,96915
Water2,450136
1
A: AA98 Fab heavy chain
B: AA98 Fab light chain
C: Cell surface glycoprotein MUC18
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, AA98 Fab is purified to homogeneity and then pooled with purified CD146 D4-D5 protein. Elution profiles of AA98 Fab, CD146 D4-D5 and complex of both are compared. Same ...Evidence: gel filtration, AA98 Fab is purified to homogeneity and then pooled with purified CD146 D4-D5 protein. Elution profiles of AA98 Fab, CD146 D4-D5 and complex of both are compared. Same result could also be found in the final crystal structure.
  • 68.9 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)68,94512
Polymers67,8223
Non-polymers1,1239
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-36 kcal/mol
Surface area28950 Å2
MethodPISA
2
L: AA98 Fab light chain
D: Cell surface glycoprotein MUC18
H: AA98 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6689
Polymers67,8223
Non-polymers8476
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-38 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.203, 88.387, 94.644
Angle α, β, γ (deg.)90.000, 89.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody AA98 Fab heavy chain


Mass: 23458.402 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 AA98 Fab light chain


Mass: 24031.615 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)

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Protein / Sugars , 2 types, 6 molecules CD

#3: Protein Cell surface glycoprotein MUC18 / CD146 / Cell surface glycoprotein P1H12 / Melanoma cell adhesion molecule / Melanoma-associated ...CD146 / Cell surface glycoprotein P1H12 / Melanoma cell adhesion molecule / Melanoma-associated antigen A32 / Melanoma-associated antigen MUC18 / S-endo 1 endothelial-associated antigen


Mass: 20331.879 Da / Num. of mol.: 2 / Fragment: domain 4, domain 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCAM, MUC18 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P43121
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 147 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, pH 7.5, 8~15% w/v Polyethylene glycol 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2015
RadiationMonochromator: CCD / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.776→30 Å / Num. obs: 30880 / % possible obs: 88.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 64.72 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.045 / Rrim(I) all: 0.104 / Χ2: 1.002 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.95.331220.70.4530.91389.9
2.9-3.025.330980.8210.3240.919900.7230.796
3.02-3.155.430910.8930.2190.97289.50.4890.539
3.15-3.325.431020.9470.1521.00689.50.3420.376
3.32-3.535.531330.9760.0891.0189.70.20.22
3.53-3.85.630980.9860.0591.02689.60.1340.147
3.8-4.185.730900.9930.0431.02188.90.0980.108
4.18-4.785.730660.9940.0340.99388.30.0770.085
4.78-6.025.830560.9960.0271.10286.80.060.066
6.02-305.930240.9990.0171.04684.60.040.044

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YEC

1yec


Resolution: 2.776→29.712 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.02
RfactorNum. reflection% reflection
Rfree0.2615 1582 5.13 %
Rwork0.2166 --
obs0.2189 30865 87.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 224.31 Å2 / Biso mean: 66.8924 Å2 / Biso min: 26.27 Å2
Refinement stepCycle: final / Resolution: 2.776→29.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9437 0 118 136 9691
Biso mean--70.22 52.1 -
Num. residues----1224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.776-2.86530.41031040.3183233176
2.8653-2.96760.35551350.3145273390
2.9676-3.08630.36291460.2945270389
3.0863-3.22660.32041490.2831271590
3.2266-3.39650.29751700.262269090
3.3965-3.6090.29221690.2386267490
3.609-3.88710.29091210.2157274289
3.8871-4.27720.2521620.1938268989
4.2772-4.89370.1961360.1752270988
4.8937-6.15660.22831740.1867261487
6.1566-29.7120.22791160.1924268385

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