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- PDB-7st5: Structure of Fab CC-95251 in complex with SIRP-alpha -

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Basic information

Entry
Database: PDB / ID: 7st5
TitleStructure of Fab CC-95251 in complex with SIRP-alpha
Components
  • (Fab CC-95251 anti-SIRP-alpha ...) x 2
  • Tyrosine-protein phosphatase non-receptor type substrate 1
KeywordsIMMUNE SYSTEM / cell surface receptor
Function / homology
Function and homology information


negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / GTPase regulator activity / cell-cell adhesion mediator activity ...negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / GTPase regulator activity / cell-cell adhesion mediator activity / protein antigen binding / negative regulation of nitric oxide biosynthetic process / negative regulation of interferon-beta production / negative regulation of JNK cascade / regulation of tumor necrosis factor production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of interleukin-6 production / tertiary granule membrane / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / positive regulation of phagocytosis / protein tyrosine kinase binding / negative regulation of protein phosphorylation / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / cellular response to type II interferon / SH3 domain binding / cellular response to hydrogen peroxide / cell migration / positive regulation of T cell activation / regulation of gene expression / cellular response to lipopolysaccharide / protein phosphatase binding / cell adhesion / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFenalti, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Cancer Res Commun / Year: 2024
Title: Discovery and Preclinical Activity of BMS-986351, an Antibody to SIRP alpha That Enhances Macrophage-mediated Tumor Phagocytosis When Combined with Opsonizing Antibodies.
Authors: Chan, H. / Trout, C.V. / Mikolon, D. / Adams, P. / Guzman, R. / Mavrommatis, K. / Abbasian, M. / Hadjivassiliou, H. / Dearth, L. / Fox, B.A. / Sivakumar, P. / Cho, H. / Hariharan, K.
History
DepositionNov 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 29, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab CC-95251 anti-SIRP-alpha heavy chain
L: Fab CC-95251 anti-SIRP-alpha light chain
F: Tyrosine-protein phosphatase non-receptor type substrate 1
h: Fab CC-95251 anti-SIRP-alpha heavy chain
l: Fab CC-95251 anti-SIRP-alpha light chain
A: Tyrosine-protein phosphatase non-receptor type substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,33913
Polymers121,8746
Non-polymers4657
Water3,027168
1
H: Fab CC-95251 anti-SIRP-alpha heavy chain
L: Fab CC-95251 anti-SIRP-alpha light chain
A: Tyrosine-protein phosphatase non-receptor type substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1536
Polymers60,9373
Non-polymers2163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-26 kcal/mol
Surface area22020 Å2
MethodPISA
2
F: Tyrosine-protein phosphatase non-receptor type substrate 1
h: Fab CC-95251 anti-SIRP-alpha heavy chain
l: Fab CC-95251 anti-SIRP-alpha light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1857
Polymers60,9373
Non-polymers2484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-19 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.957, 97.704, 103.385
Angle α, β, γ (deg.)77.180, 85.920, 85.740
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21h
12L
22l
13F
23A

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALPROPROHA2 - 2202 - 220
21VALVALPROPROhD2 - 2202 - 220
12ASPASPARGARGLB1 - 2111 - 211
22ASPASPARGARGlE1 - 2111 - 211
13GLUGLUGLUGLUFC3 - 1113 - 111
23GLUGLUGLUGLUAF3 - 1113 - 111

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules FA

#3: Protein Tyrosine-protein phosphatase non-receptor type substrate 1 / SHP substrate 1 / SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / ...SHP substrate 1 / SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / CD172 antigen-like family member A / Inhibitory receptor SHPS-1 / Macrophage fusion receptor / MyD-1 antigen / Signal-regulatory protein alpha-1 / Sirp-alpha-1 / Signal-regulatory protein alpha-2 / Sirp-alpha-2 / Signal-regulatory protein alpha-3 / Sirp-alpha-3 / p84


Mass: 13598.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP / Production host: Homo sapiens (human) / References: UniProt: P78324

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Antibody , 2 types, 4 molecules HhLl

#1: Antibody Fab CC-95251 anti-SIRP-alpha heavy chain


Mass: 24223.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab CC-95251 anti-SIRP-alpha light chain


Mass: 23115.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 175 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH 6.5, 25 %w/v PEG MME 550, 0.01 M Zinc sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.0782 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 11, 2016 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 2.1→95 Å / Num. obs: 83446 / % possible obs: 88.6 % / Redundancy: 2.2 % / CC1/2: 0.996 / Net I/σ(I): 6.3
Reflection shellResolution: 2.11→2.22 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12639 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JJS

2jjs


Resolution: 2.2→50.01 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.284 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 3601 4.9 %RANDOM
Rwork0.2446 ---
obs0.2463 69503 88.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.28 Å2 / Biso mean: 41.674 Å2 / Biso min: 13.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å21.33 Å20.52 Å2
2--0.15 Å2-0.48 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 2.2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7446 0 30 168 7644
Biso mean--49.93 39.76 -
Num. residues----1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.027647
X-RAY DIFFRACTIONr_bond_other_d0.0040.026675
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.93810427
X-RAY DIFFRACTIONr_angle_other_deg1.106315254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21551026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49623.532269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50815993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461531
X-RAY DIFFRACTIONr_chiral_restr0.1020.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218827
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021752
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11H191340.05
12h191340.05
21L195520.04
22l195520.04
31F97720.05
32A97720.05
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 154 -
Rwork0.35 3304 -
all-3458 -
obs--55.86 %

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