[English] 日本語
Yorodumi
- PDB-5iwl: CD47-diabody complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iwl
TitleCD47-diabody complex
Components
  • 5F9 diabody
  • Leukocyte surface antigen CD47
KeywordsCELL ADHESION / receptor / diabody / 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 / regulation of type II interferon production / cell-cell adhesion mediator activity / ATP export / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of tumor necrosis factor production ...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 / regulation of type II interferon production / cell-cell adhesion mediator activity / ATP export / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / thrombospondin receptor activity / tertiary granule membrane / Integrin cell surface interactions / cellular response to interleukin-1 / specific granule membrane / positive regulation of phagocytosis / positive regulation of stress fiber assembly / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of T cell activation / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsDi, W. / Jude, K.M. / Garcia, K.C.
CitationJournal: J.Clin.Invest. / Year: 2016
Title: CD47-blocking immunotherapies stimulate macrophage-mediated destruction of small-cell lung cancer.
Authors: Weiskopf, K. / Jahchan, N.S. / Schnorr, P.J. / Cristea, S. / Ring, A.M. / Maute, R.L. / Volkmer, A.K. / Volkmer, J.P. / Liu, J. / Lim, J.S. / Yang, D. / Seitz, G. / Nguyen, T. / Wu, D. / ...Authors: Weiskopf, K. / Jahchan, N.S. / Schnorr, P.J. / Cristea, S. / Ring, A.M. / Maute, R.L. / Volkmer, A.K. / Volkmer, J.P. / Liu, J. / Lim, J.S. / Yang, D. / Seitz, G. / Nguyen, T. / Wu, D. / Jude, K. / Guerston, H. / Barkal, A. / Trapani, F. / George, J. / Poirier, J.T. / Gardner, E.E. / Miles, L.A. / de Stanchina, E. / Lofgren, S.M. / Vogel, H. / Winslow, M.M. / Dive, C. / Thomas, R.K. / Rudin, C.M. / van de Rijn, M. / Majeti, R. / Garcia, K.C. / Weissman, I.L. / Sage, J.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 2.0Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / citation ...chem_comp / citation / entity_poly / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5F9 diabody
A: 5F9 diabody
C: Leukocyte surface antigen CD47
D: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,36512
Polymers76,7384
Non-polymers1,6288
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.280, 103.280, 131.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Antibody 5F9 diabody


Mass: 25510.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody Leukocyte surface antigen CD47 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 12858.470 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 19-132) / Mutation: C15G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08722
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6 / Details: sodium cacodylate pH 6.0, 17% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127085 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127085 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 20405 / % possible obs: 99.9 % / Redundancy: 10.8 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 10.8 % / Rmerge(I) obs: 2.562 / Mean I/σ(I) obs: 0.95 / % possible all: 99.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHASER2.5.6phasing
PHENIX1.10 r2155refinement
PDB_EXTRACT3.15data extraction
XDSJune 17, 2015data reduction
XDSJune 17, 2015data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→44.722 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / Phase error: 28.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 1299 6.37 %
Rwork0.2211 19083 -
obs0.224 20382 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.43 Å2 / Biso mean: 64.6616 Å2 / Biso min: 24.37 Å2
Refinement stepCycle: final / Resolution: 2.8→44.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 104 7 5361
Biso mean--74.97 35.07 -
Num. residues----694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035488
X-RAY DIFFRACTIONf_angle_d0.6177479
X-RAY DIFFRACTIONf_chiral_restr0.046851
X-RAY DIFFRACTIONf_plane_restr0.004955
X-RAY DIFFRACTIONf_dihedral_angle_d12.1223197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8002-2.91230.33681440.343420692213100
2.9123-3.04480.32071390.306120922231100
3.0448-3.20530.33951450.2921032248100
3.2053-3.4060.34771450.265320962241100
3.406-3.66890.27611390.23520902229100
3.6689-4.03790.26051420.216721252267100
4.0379-4.62160.2531500.182721212271100
4.6216-5.82080.22431450.174821492294100
5.8208-44.72720.21821500.19592238238899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9182.0577-1.04181.9594-0.41114.8413-0.1693-0.16490.2169-0.0053-0.0984-0.1373-0.14090.04160.24140.4941-0.0087-0.08030.25280.04990.4866-27.5823.6659-0.1524
25.1932-0.0221-1.14255.1406-0.81123.159-0.51050.2651-0.8645-0.58910.3617-0.33350.80670.35120.10590.7151-0.09660.22010.4426-0.08820.65138.657925.839711.4597
36.31152.0656-0.24931.6318-0.46842.0526-0.05420.03040.0623-0.06660.04260.05660.05360.11770.04680.3916-0.04690.05620.3282-0.00510.3793-7.841135.563922.3254
42.9938-1.1751-0.04462.2639-1.37863.0009-0.04150.1479-0.406-0.6477-0.1820.08021.12970.26350.22220.73010.03230.03170.301-0.00390.5424-27.85624.714610.9803
54.916-2.9435-4.7191.78962.86254.53010.2315-0.35370.26010.48110.8810.9966-0.6333-1.0377-0.83780.47310.17210.15291.06520.32590.7015-55.243522.02319.5697
67.15642.63231.10278.40041.70647.58890.17040.27091.11470.6170.77741.64440.2201-2.4501-1.05730.4748-0.0791-0.0061.32740.35040.7931-70.1216.761321.2029
75.54911.9625-3.28793.3664-5.44288.724-0.23480.92980.2208-1.20760.08710.02530.9129-2.27130.45440.5809-0.306-0.08810.91960.19110.5804-52.867511.00194.916
88.6174-6.0806-5.53635.21861.98468.3608-0.1786-0.05180.4468-0.25190.5027-0.93230.47390.0166-0.32510.6452-0.0858-0.02220.36060.02130.4527-52.32737.104918.8486
91.1303-0.61770.06315.2222-3.5992.6945-0.54460.8404-0.0109-0.48961.00160.6109-0.399-1.5365-0.6110.5647-0.1287-0.14210.8797-0.04470.3994-59.46327.409815.8411
100.3043-1.5647-1.088.43345.74363.91810.34020.14290.05610.82960.8389-0.4110.2074-0.12-1.14550.5634-0.0646-0.02560.54180.10580.6104-65.782211.312225.111
112.536-3.0261-4.43464.20524.20569.02570.20180.70360.4637-0.3337-0.06520.049-0.4685-1.2593-0.17630.45450.0192-0.09510.46660.06520.5555-52.608714.850216.979
121.90420.9045-2.78061.76620.14727.580.4653-0.07191.18070.23910.64210.0171-0.1203-0.6141-0.90930.55370.1113-0.00180.6120.16130.5842-56.761420.09717.7973
130.9676-2.03712.1055.3194-3.54245.29340.2351-0.18360.18370.1180.3242-0.4601-0.1727-0.2804-0.30020.56970.16840.02670.5168-0.10610.41238.684858.095812.7069
146.6358-5.06941.43736.10581.36723.0283-0.02060.17961.56190.19160.54760.2207-1.10110.3964-0.69340.68-0.05930.15660.41080.05230.600821.1367.63650.9079
153.5332-0.78781.20428.3271.63592.44970.8419-0.1817-0.36250.5057-0.35890.4127-0.04191.1311-0.6350.327-0.06130.12610.5573-0.05010.629415.038452.459317.5271
162.3681-1.0463-1.14377.7234-4.01846.7008-0.3339-0.1834-0.3680.18380.22680.11370.2184-0.48620.06790.29110.00090.08410.4592-0.01880.480919.373446.95364.9869
175.8368-0.6541-4.08642.3625-0.08643.04530.2413-0.06210.3936-0.16130.1371-0.1264-0.03390.6117-0.71820.3685-0.0133-0.08970.31540.01690.481623.161753.68476.7039
184.74412.17833.60555.53410.4223.10870.819-1.0028-0.8870.0427-0.1727-0.5754-0.1764-0.9878-0.75010.4232-0.02640.09570.44340.07070.379123.210361.0372-2.4689
191.70571.8327-1.9583.5466-0.19094.4292-0.04810.10560.25170.10770.62770.6403-0.29510.1295-0.78830.34250.0890.01140.44860.01730.445112.952752.17355.1104
204.43163.8385-3.68825.2947-5.54019.71730.140.19930.5842-0.46990.47830.50860.3837-0.1681-0.50530.4467-0.0010.08270.3931-0.03310.427110.875558.91014.1182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 125 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 126 through 233 )B0
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 125 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 233 )A0
5X-RAY DIFFRACTION5chain 'C' and (resid 2 through 8 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 9 through 21 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 22 through 36 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 37 through 58 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 59 through 79 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 80 through 89 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 90 through 102 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 103 through 114 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 8 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 9 through 21 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 22 through 32 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 33 through 58 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 59 through 79 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 80 through 89 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 90 through 102 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 103 through 114 )D0

+
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