[English] 日本語
Yorodumi
- PDB-8zca: Crystal structure of human CD47 ECD bound to Fab of Hu1C8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zca
TitleCrystal structure of human CD47 ECD bound to Fab of Hu1C8
Components
  • 1C8 Fab heavy chain
  • 1C8 Fab light chain
  • Leukocyte surface antigen CD47
KeywordsIMMUNE SYSTEM / CD47 / antibody
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 phagocytosis / positive regulation of stress fiber assembly / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cellular response to type II interferon / positive regulation of T cell activation / positive regulation of inflammatory response / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, Z. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The humanized antibody Hu1C8 binds to a distinct epitope of CD47 in a novel metal ion-dependent manner to induce low RBC toxicity and effective antitumour activity
Authors: Lu, X. / Sun, B.
History
DepositionApr 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1C8 Fab light chain
D: 1C8 Fab heavy chain
B: 1C8 Fab light chain
C: 1C8 Fab heavy chain
E: Leukocyte surface antigen CD47
F: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,12214
Polymers124,9736
Non-polymers1,1498
Water3,063170
1
A: 1C8 Fab light chain
D: 1C8 Fab heavy chain
F: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0617
Polymers62,4873
Non-polymers5754
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1C8 Fab light chain
C: 1C8 Fab heavy chain
E: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0617
Polymers62,4873
Non-polymers5754
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.224, 79.931, 92.751
Angle α, β, γ (deg.)112.50, 96.61, 103.16
Int Tables number1
Space group name H-MP1

-
Components

-
Antibody , 2 types, 4 molecules ABDC

#1: Antibody 1C8 Fab light chain


Mass: 23801.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 1C8 Fab heavy chain


Mass: 23760.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Protein / Sugars , 2 types, 6 molecules EF

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


Mass: 14924.716 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q08722
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

-
Non-polymers , 3 types, 174 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.0) and 20% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38158 / % possible obs: 97.7 % / Redundancy: 2.8 % / CC1/2: 0.926 / CC star: 0.981 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.109 / Rrim(I) all: 0.197 / Χ2: 1.127 / Net I/σ(I): 4.8 / Num. measured all: 108179
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.542.20.35716710.8540.960.2680.4490.56686.9
2.54-2.592.40.32719120.8830.9680.2420.4090.55896.2
2.59-2.642.40.3519040.8870.970.2570.4360.58197.7
2.64-2.692.60.32319030.8740.9660.230.3990.61497.8
2.69-2.752.70.35719250.8320.9530.2520.4390.66598
2.75-2.822.70.31319290.8780.9670.2170.3830.69298.1
2.82-2.892.70.30418850.8570.9610.210.3710.70998.1
2.89-2.962.70.26719490.9140.9770.1850.3270.80498.2
2.96-3.052.70.27318890.8770.9670.1930.3370.88798.4
3.05-3.1530.28719200.8620.9620.1940.3481.00197.9
3.15-3.262.90.22619060.910.9760.1550.2751.00598.6
3.26-3.393.10.2219440.9140.9770.1470.2661.13198.5
3.39-3.553.10.22719210.9470.9860.1490.2721.1998.6
3.55-3.733.10.25619540.8120.9470.170.3081.43998.5
3.73-3.9730.18519010.8710.9650.1260.2251.48198.7
3.97-4.273.10.14119250.9390.9840.0940.171.64598.7
4.27-4.73.10.12619470.9610.990.0830.1521.86198.9
4.7-5.383.10.11519310.9510.9870.0760.1381.64698.9
5.38-6.7830.11619250.9310.9820.0790.1411.36698.9
6.78-503.10.08719170.980.9950.0580.1051.56297.6

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000phasing
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→38.52 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 33.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2663 1902 5.24 %
Rwork0.2146 --
obs0.2174 36287 91.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8341 0 56 170 8567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098572
X-RAY DIFFRACTIONf_angle_d1.04511631
X-RAY DIFFRACTIONf_dihedral_angle_d7.0671202
X-RAY DIFFRACTIONf_chiral_restr0.0561326
X-RAY DIFFRACTIONf_plane_restr0.0091470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.4217910.30941518X-RAY DIFFRACTION57
2.55-2.620.32961250.29332264X-RAY DIFFRACTION84
2.62-2.70.31571350.27952295X-RAY DIFFRACTION85
2.7-2.790.37751250.27742382X-RAY DIFFRACTION88
2.79-2.890.33241380.27782484X-RAY DIFFRACTION92
2.89-30.27941320.27392513X-RAY DIFFRACTION92
3-3.140.37211430.27152522X-RAY DIFFRACTION95
3.14-3.30.27611400.252584X-RAY DIFFRACTION96
3.3-3.510.30721500.24322639X-RAY DIFFRACTION97
3.51-3.780.29231450.21312643X-RAY DIFFRACTION98
3.78-4.160.26811460.19212635X-RAY DIFFRACTION98
4.16-4.760.21781400.1642648X-RAY DIFFRACTION99
4.76-60.2111480.17372645X-RAY DIFFRACTION98
6-38.520.18941440.17122613X-RAY DIFFRACTION97

+
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