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- PDB-7xjf: Crystal structure of 6MW3211 Fab in complex with CD47 -

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Basic information

Entry
Database: PDB / ID: 7xjf
TitleCrystal structure of 6MW3211 Fab in complex with CD47
Components
  • Heavy chain of 6MW3211 Fab
  • Leukocyte surface antigen CD47
  • Light chain of 6MW3211 Fab
KeywordsIMMUNE SYSTEM / CD47 / antibody / Fab
Function / homology
Function and homology information


cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / cell-cell adhesion mediator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of type II interferon production / ATP export / fibrinogen binding ...cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / cell-cell adhesion mediator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of type II interferon production / ATP export / fibrinogen binding / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of phagocytosis / thrombospondin receptor activity / tertiary granule membrane / cellular response to interleukin-1 / Integrin cell surface interactions / specific granule membrane / positive regulation of phagocytosis / positive regulation of stress fiber assembly / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cellular response to type II interferon / positive regulation of T cell activation / positive regulation of inflammatory response / cell migration / angiogenesis / inflammatory response / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWang, J. / Wang, R. / Jiao, S. / Wang, S. / Zhang, J. / Zhang, M. / Wang, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Theranostics / Year: 2023
Title: Blockade of dual immune checkpoint inhibitory signals with a CD47/PD-L1 bispecific antibody for cancer treatment.
Authors: Wang, R. / Zhang, C. / Cao, Y. / Wang, J. / Jiao, S. / Zhang, J. / Wang, M. / Tang, P. / Ouyang, Z. / Liang, W. / Mao, Y. / Wang, A. / Li, G. / Zhang, J. / Wang, M. / Wang, S. / Gui, X.
History
DepositionApr 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of 6MW3211 Fab
B: Light chain of 6MW3211 Fab
C: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5889
Polymers60,9903
Non-polymers1,5976
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-15 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.830, 100.480, 163.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 3 types, 3 molecules ABC

#1: Antibody Heavy chain of 6MW3211 Fab


Mass: 24472.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain of 6MW3211 Fab


Mass: 23429.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Leukocyte surface antigen CD47 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 13087.788 Da / Num. of mol.: 1 / Mutation: C33G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Cell (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q08722

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Sugars , 3 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: 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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 2 types, 254 molecules

#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.2 M DL-malic acid, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 31874 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.043 / Rrim(I) all: 0.136 / Χ2: 0.999 / Net I/σ(I): 5.9 / Num. measured all: 311060
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6910.41.0131330.8280.3321.0640.947100
2.69-2.810.30.7631420.8780.2520.8020.911100
2.8-2.93100.54131350.930.1810.5720.935100
2.93-3.089.60.34331430.9710.1170.3630.936100
3.08-3.289.60.22931380.9860.0780.2431.01899.5
3.28-3.5310.20.14631490.9940.0480.1541.023100
3.53-3.889.90.10331880.9960.0340.1091.049100
3.88-4.459.40.07331940.9970.0250.0781.068100
4.45-5.69.70.06132430.9980.020.0641.018100
5.6-508.70.05734090.9980.020.0611.09999.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZU, 6JJP

5tzu

6jjp


Resolution: 2.6→40.83 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1702 5.4 %
Rwork0.1872 29841 -
obs0.1896 31543 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.14 Å2 / Biso mean: 35.8626 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 2.6→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4274 0 102 252 4628
Biso mean--74.96 34.27 -
Num. residues----555
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.680.34321410.304824692610100
2.68-2.760.35911450.285824392584100
2.76-2.860.32291450.262724472592100
2.86-2.980.31351450.237724262571100
2.98-3.110.28371420.224824532595100
3.11-3.280.25571320.203724562588100
3.28-3.480.24621300.186124952625100
3.48-3.750.20091580.157724582616100
3.75-4.130.1961160.146925182634100
4.13-4.720.15141580.127825062664100
4.72-5.950.18151370.143625352672100
5.95-40.830.21841530.19342639279299

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