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- PDB-6nmu: Kick-Off Fab 115 anti-SIRP-alpha antibody in complex with SIRP-al... -

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Basic information

Entry
Database: PDB / ID: 6nmu
TitleKick-Off Fab 115 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1
Components
  • Fab 115 anti-SIRP-alpha antibody Variable Heavy Chain
  • Fab 115 anti-SIRP-alpha antibody Variable Light Chain
  • Tyrosine-protein phosphatase non-receptor type substrate 1
KeywordsIMMUNE SYSTEM / SIRP-alpha / Signal regulatory protein alpha / Signal-regulatory protein alpha / Tyrosine-protein phosphatase non-receptor type substrate 1 / CD47 / Cluster of Differentiation 47 / anti-SIRP-alpha antibody / Blocking anti-SIRP-alpha antibody / Non-Blocking anti-SIRP-alpha antibody / Kick-Off anti-SIRP-alpha antibody / anti-SIRP-alpha antibody in complex with SIRP-alpha
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å
AuthorsWibowo, A.S. / Carter, J.J. / Sim, J.
CitationJournal: Mabs / Year: 2019
Title: Discovery of high affinity, pan-allelic, and pan-mammalian reactive antibodies against the myeloid checkpoint receptor SIRP alpha.
Authors: Sim, J. / Sockolosky, J.T. / Sangalang, E. / Izquierdo, S. / Pedersen, D. / Harriman, W. / Wibowo, A.S. / Carter, J. / Madan, A. / Doyle, L. / Harrabi, O. / Kauder, S.E. / Chen, A. / Kuo, T. ...Authors: Sim, J. / Sockolosky, J.T. / Sangalang, E. / Izquierdo, S. / Pedersen, D. / Harriman, W. / Wibowo, A.S. / Carter, J. / Madan, A. / Doyle, L. / Harrabi, O. / Kauder, S.E. / Chen, A. / Kuo, T.C. / Wan, H. / Pons, J.
History
DepositionJan 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 115 anti-SIRP-alpha antibody Variable Light Chain
H: Fab 115 anti-SIRP-alpha antibody Variable Heavy Chain
S: Tyrosine-protein phosphatase non-receptor type substrate 1
A: Fab 115 anti-SIRP-alpha antibody Variable Light Chain
B: Fab 115 anti-SIRP-alpha antibody Variable Heavy Chain
C: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)124,0626
Polymers124,0626
Non-polymers00
Water4,882271
1
L: Fab 115 anti-SIRP-alpha antibody Variable Light Chain
H: Fab 115 anti-SIRP-alpha antibody Variable Heavy Chain
S: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)62,0313
Polymers62,0313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-29 kcal/mol
Surface area24550 Å2
MethodPISA
2
A: Fab 115 anti-SIRP-alpha antibody Variable Light Chain
B: Fab 115 anti-SIRP-alpha antibody Variable Heavy Chain
C: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)62,0313
Polymers62,0313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-29 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.931, 71.742, 77.731
Angle α, β, γ (deg.)98.890, 103.260, 90.070
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Fab 115 anti-SIRP-alpha antibody Variable Light Chain


Mass: 23575.086 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 115 anti-SIRP-alpha antibody Variable Heavy Chain


Mass: 24424.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Tyrosine-protein phosphatase non-receptor type substrate 1 / SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / CD172 antigen-like ...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: 14031.807 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1 M Tris, 0.2 M MgCl2, 18% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.55→74.7 Å / Num. obs: 36050 / % possible obs: 94.8 % / Redundancy: 1.9 % / Rsym value: 0.13 / Net I/σ(I): 5.9
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3144 / Rsym value: 0.661 / % possible all: 82.4

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.55→74.7 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.879 / SU B: 14.496 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 9.868 / ESU R Free: 0.346
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 1835 5.1 %RANDOM
Rwork0.1929 ---
obs0.1964 34215 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.57 Å2 / Biso mean: 39.929 Å2 / Biso min: 8.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.03 Å20.04 Å2
2--0 Å20.02 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.55→74.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8277 0 0 271 8548
Biso mean---32.06 -
Num. residues----1087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028473
X-RAY DIFFRACTIONr_bond_other_d0.0020.027606
X-RAY DIFFRACTIONr_angle_refined_deg1.561.95211524
X-RAY DIFFRACTIONr_angle_other_deg0.948317708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.62851079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84723.851348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.488151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3291548
X-RAY DIFFRACTIONr_chiral_restr0.0820.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021737
LS refinement shellResolution: 2.554→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 95 -
Rwork0.289 1885 -
all-1980 -
obs--70.06 %

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