[English] 日本語
Yorodumi
- PDB-1h03: Human CD55 domains 3 & 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h03
TitleHuman CD55 domains 3 & 4
ComponentsCOMPLEMENT DECAY-ACCELERATING FACTOR
KeywordsIMMUNE SYSTEM PROTEIN / COMPLEMENT DECAY ACCELERATING FACTOR / ENTEROVIRAL RECEPTOR / BACTERIAL RECEPTOR / LIGAND FOR CD97 / COMPLEMENT PATHWAY / ALTERNATIVE SPLICING / GPI-ANCHOR
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / complement activation, classical pathway ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / complement activation, classical pathway / transport vesicle / side of membrane / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / positive regulation of cytosolic calcium ion concentration / virus receptor activity / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Complement decay-accelerating factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.7 Å
AuthorsWilliams, P. / Chaudhry, Y. / Goodfellow, I. / Billington, J. / Spiller, B. / Evans, D.J. / Lea, S.M.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Mapping Cd55 Function. The Structure of Two Pathogen-Binding Domains at 1.7 A
Authors: Williams, P. / Chaudhry, Y. / Goodfellow, I. / Billington, J. / Powell, R. / Spiller, O. / Evans, D.J. / Lea, S.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of a Biologically Active Fragment of Cd55
Authors: Lea, S.M. / Powell, R. / Evans, D.J.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: Determination of the Affinity and Kinetic Constants for the Interaction between the Human Virus Echovirus 11 and its Cellular Receptor, Cd55
Authors: Lea, S.M. / Powell, R. / Mckee, T. / Evans, D.J. / Brown, D.J. / Stuart, D.I. / Van Der Merwe, A.
History
DepositionJun 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: COMPLEMENT DECAY-ACCELERATING FACTOR
Q: COMPLEMENT DECAY-ACCELERATING FACTOR


Theoretical massNumber of molelcules
Total (without water)27,1722
Polymers27,1722
Non-polymers00
Water3,171176
1
P: COMPLEMENT DECAY-ACCELERATING FACTOR


Theoretical massNumber of molelcules
Total (without water)13,5861
Polymers13,5861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
Q: COMPLEMENT DECAY-ACCELERATING FACTOR


Theoretical massNumber of molelcules
Total (without water)13,5861
Polymers13,5861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.620, 38.770, 45.330
Angle α, β, γ (deg.)110.48, 96.55, 108.90
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein COMPLEMENT DECAY-ACCELERATING FACTOR / CD55 ANTIGEN / CD55 / DAF


Mass: 13586.049 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR SCR DOMAINS 3 & 4, RESIDUES 161-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P08174
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRECOGNIZES C4B AND C3B FRAGMENTS GENERATED DURING C4 AND C3 ACTIVATION. PART OF THE COMPLEMENT ...RECOGNIZES C4B AND C3B FRAGMENTS GENERATED DURING C4 AND C3 ACTIVATION. PART OF THE COMPLEMENT CASCADE IN IMMNUNITY.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, sitting drop
Details: Lea, S.M., (1999) Acta Crystallogr.,Sect.D, D55, 1198.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %PEG40001reservoir
20.2 Msodium acetate1reservoir
30.1 Msodium acetate trihydrate1reservoirpH4.6
48-12 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 44162 / % possible obs: 100 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 92
Reflection
*PLUS
Num. measured all: 685390
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.35

-
Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 -5 %RANDOM
Rwork0.191 ---
obs0.191 44162 100 %-
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-8.5 Å2-2.2 Å2-7.4 Å2
2---4.1 Å2-7.8 Å2
3----4.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 0 176 2078
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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