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- PDB-7wn8: Crystal structure of antibody (BC31M5) binds to CD47 -

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Basic information

Entry
Database: PDB / ID: 7wn8
TitleCrystal structure of antibody (BC31M5) binds to CD47
Components
  • BC31M5 Fab Heavy chain
  • BC31M5 Fab Light chain
  • Leukocyte surface antigen CD47
KeywordsANTITUMOR PROTEIN / Fab / human CD47 / Complex
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 stress fiber assembly / positive regulation of phagocytosis / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / positive regulation of T cell activation / cellular response to type II interferon / positive regulation of inflammatory response / cell migration / angiogenesis / inflammatory response / positive regulation of cell population proliferation / apoptotic process / 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: 2.8 Å
AuthorsLi, Y. / Wang, W. / Sui, J. / Zhang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2012CB837600 China
CitationJournal: J Hematol Oncol / Year: 2023
Title: A pH-dependent anti-CD47 antibody that selectively targets solid tumors and improves therapeutic efficacy and safety.
Authors: Li, Y. / Liu, J. / Chen, W. / Wang, W. / Yang, F. / Liu, X. / Sheng, Y. / Du, K. / He, M. / Lyu, X. / Li, H. / Zhao, L. / Wei, Z. / Wang, F. / Zheng, S. / Sui, J.
History
DepositionJan 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: Leukocyte surface antigen CD47
C: Leukocyte surface antigen CD47
H: BC31M5 Fab Heavy chain
L: BC31M5 Fab Light chain
P: BC31M5 Fab Heavy chain
Q: BC31M5 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,62214
Polymers167,0986
Non-polymers5238
Water3,459192
1
A: Leukocyte surface antigen CD47
H: BC31M5 Fab Heavy chain
L: BC31M5 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8768
Polymers83,5493
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-198 kcal/mol
Surface area24400 Å2
MethodPISA
2
C: Leukocyte surface antigen CD47
P: BC31M5 Fab Heavy chain
Q: BC31M5 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7456
Polymers83,5493
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-128 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.402, 94.281, 174.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leukocyte surface antigen CD47 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 35195.395 Da / Num. of mol.: 2 / Mutation: C15G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q08722
#2: Antibody BC31M5 Fab Heavy chain


Mass: 24686.543 Da / Num. of mol.: 2
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 BC31M5 Fab Light chain


Mass: 23667.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M Zinc acetate dihydrate, 0.1M Sodium cacodylate trihydrate (pH 6.5), 18% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→49.59 Å / Num. obs: 37875 / % possible obs: 99.76 % / Redundancy: 13.2 % / Biso Wilson estimate: 49.49 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1613 / Rpim(I) all: 0.04583 / Rrim(I) all: 0.1677 / Net I/σ(I): 16.96
Reflection shellResolution: 2.801→2.901 Å / Num. unique obs: 3664 / CC1/2: 0.848 / CC star: 0.958

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZT, 4JPK

5tzt

4jpk


Resolution: 2.8→49.59 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 1999 5.28 %
Rwork0.2434 35871 -
obs0.2451 37870 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.23 Å2 / Biso mean: 44.4171 Å2 / Biso min: 13 Å2
Refinement stepCycle: final / Resolution: 2.8→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8144 0 8 192 8344
Biso mean--80.09 40.43 -
Num. residues----1060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.870.46411260.38492506263298
2.87-2.950.33321480.331425072655100
2.95-3.040.30291440.291825282672100
3.04-3.130.30891410.283425282669100
3.13-3.240.31491380.281825232661100
3.25-3.370.36291400.286625662706100
3.37-3.530.2741420.262225272669100
3.53-3.710.31541380.246425392677100
3.71-3.950.26951490.241625532702100
3.95-4.250.27471400.218125642704100
4.25-4.680.1791430.177125812724100
4.68-5.360.21761440.17925912735100
5.36-6.740.24511500.238626232773100
6.75-49.590.28951560.248627352891100

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