[English] 日本語
Yorodumi
- PDB-6nms: Blocking Fab 136 anti-SIRP-alpha antibody in complex with SIRP-al... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nms
TitleBlocking Fab 136 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1
Components
  • Fab 136 anti-SIRP-alpha antibody Variable Heavy Chain
  • Fab 136 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 / SH3 domain binding / cellular response to type II interferon / cellular response to hydrogen peroxide / cell migration / positive regulation of T cell activation / regulation of gene expression / protein phosphatase binding / cellular response to lipopolysaccharide / 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: 2.11 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
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Fab 136 anti-SIRP-alpha antibody Variable Light Chain
H: Fab 136 anti-SIRP-alpha antibody Variable Heavy Chain
S: Tyrosine-protein phosphatase non-receptor type substrate 1
A: Fab 136 anti-SIRP-alpha antibody Variable Light Chain
B: Fab 136 anti-SIRP-alpha antibody Variable Heavy Chain
C: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)124,4256
Polymers124,4256
Non-polymers00
Water6,107339
1
L: Fab 136 anti-SIRP-alpha antibody Variable Light Chain
H: Fab 136 anti-SIRP-alpha antibody Variable Heavy Chain
S: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)62,2123
Polymers62,2123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fab 136 anti-SIRP-alpha antibody Variable Light Chain
B: Fab 136 anti-SIRP-alpha antibody Variable Heavy Chain
C: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)62,2123
Polymers62,2123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.390, 75.190, 103.820
Angle α, β, γ (deg.)90.000, 104.430, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 2 through 56 or resid 58...
21(chain H and (resid 2 through 56 or resid 58...
12(chain L and (resid 1 through 80 or resid 82 through 126 or resid 128 through 214))
22(chain A and (resid 1 through 80 or resid 82 through 126 or resid 128 through 214))
13(chain C and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))
23(chain S and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resid 2 through 56 or resid 58...B2 - 56
121(chain B and (resid 2 through 56 or resid 58...B58 - 100
131(chain B and (resid 2 through 56 or resid 58...B102 - 134
141(chain B and (resid 2 through 56 or resid 58...B213 - 215
151(chain B and (resid 2 through 56 or resid 58...B213 - 215
161(chain B and (resid 2 through 56 or resid 58...B217 - 219
211(chain H and (resid 2 through 56 or resid 58...H2 - 56
221(chain H and (resid 2 through 56 or resid 58...H58 - 100
231(chain H and (resid 2 through 56 or resid 58...H102 - 6
241(chain H and (resid 2 through 56 or resid 58...H0
251(chain H and (resid 2 through 56 or resid 58...H213 - 215
261(chain H and (resid 2 through 56 or resid 58...H217 - 219
112(chain L and (resid 1 through 80 or resid 82 through 126 or resid 128 through 214))L1 - 80
122(chain L and (resid 1 through 80 or resid 82 through 126 or resid 128 through 214))L82 - 126
132(chain L and (resid 1 through 80 or resid 82 through 126 or resid 128 through 214))L128 - 214
212(chain A and (resid 1 through 80 or resid 82 through 126 or resid 128 through 214))A1 - 80
222(chain A and (resid 1 through 80 or resid 82 through 126 or resid 128 through 214))A82 - 126
232(chain A and (resid 1 through 80 or resid 82 through 126 or resid 128 through 214))A128 - 214
113(chain C and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))C2
123(chain C and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))C4 - 30
133(chain C and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))C32 - 67
143(chain C and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))C69 - 116
213(chain S and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))S2
223(chain S and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))S4 - 30
233(chain S and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))S32 - 67
243(chain S and (resid 2 or resid 4 through 30 or resid 32 through 67 or resid 69 through 116))S69 - 116

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody Fab 136 anti-SIRP-alpha antibody Variable Light Chain


Mass: 23557.102 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 136 anti-SIRP-alpha antibody Variable Heavy Chain


Mass: 24623.408 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 / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 0.2 M MgCl2, 15% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 25, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.11→50.272 Å / Num. obs: 68779 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rsym value: 0.078 / Net I/σ(I): 8.7
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 3.7 % / Num. unique obs: 5042 / Rsym value: 0.0163 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
autoPROCdata scaling
PHASERphasing
RefinementResolution: 2.11→50.272 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.36
RfactorNum. reflection% reflection
Rfree0.2438 3401 4.95 %
Rwork0.2042 --
obs0.2063 68745 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.4 Å2 / Biso mean: 55.8935 Å2 / Biso min: 28 Å2
Refinement stepCycle: final / Resolution: 2.11→50.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8274 0 0 339 8613
Biso mean---52.62 -
Num. residues----1094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078466
X-RAY DIFFRACTIONf_angle_d1.08411528
X-RAY DIFFRACTIONf_chiral_restr0.0711301
X-RAY DIFFRACTIONf_plane_restr0.0091491
X-RAY DIFFRACTIONf_dihedral_angle_d7.7545024
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1840X-RAY DIFFRACTION7.956TORSIONAL
12H1840X-RAY DIFFRACTION7.956TORSIONAL
21L1984X-RAY DIFFRACTION7.956TORSIONAL
22A1984X-RAY DIFFRACTION7.956TORSIONAL
31C992X-RAY DIFFRACTION7.956TORSIONAL
32S992X-RAY DIFFRACTION7.956TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.14020.34681400.32052722286297
2.1402-2.17210.36951420.31372697283998
2.1721-2.2060.35071360.31032705284198
2.206-2.24220.35421350.31012666280198
2.2422-2.28090.36341380.31152713285198
2.2809-2.32230.36581350.29842711284698
2.3223-2.3670.30311350.28972712284798
2.367-2.41530.3311200.28382730285098
2.4153-2.46780.2981510.27382703285498
2.4678-2.52530.33141490.27522685283498
2.5253-2.58840.281170.2642750286798
2.5884-2.65840.30791480.26432702285098
2.6584-2.73660.34571330.2592726285998
2.7366-2.82490.32781620.25222700286298
2.8249-2.92590.31031470.26222731287899
2.9259-3.0430.31591530.24312727288098
3.043-3.18150.3021460.24542708285499
3.1815-3.34920.26121350.23362761289699
3.3492-3.5590.26061460.21262738288498
3.559-3.83370.24921500.19512724287499
3.8337-4.21930.22321280.172762289099
4.2193-4.82940.18521510.13572742289398
4.8294-6.08290.15581340.14622771290598
6.0829-50.28660.16661700.14732758292897

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more