[English] 日本語
Yorodumi
- PDB-2g7i: Structure of Human Complement Factor H Carboxyl Terminal Domains ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g7i
TitleStructure of Human Complement Factor H Carboxyl Terminal Domains 19-20: a Basis for Atypical Hemolytic Uremic Syndrome
ComponentsComplement factor H
KeywordsIMMUNE SYSTEM / Sushi (CCP/SCR) domain / Complement / Regulator / Factor H / Beta-1H Globulin / Atypical Hemolytic Uremic Syndrome / Heparin Binding
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement component C3b binding / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / regulation of complement activation / complement component C3b binding / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsJaakola, V.-P. / Jokiranta, T.S. / Goldman, A.
CitationJournal: Embo J. / Year: 2006
Title: Structure of complement factor H carboxyl-terminus reveals molecular basis of atypical haemolytic uremic syndrome.
Authors: Jokiranta, T.S. / Jaakola, V.-P. / Lehtinen, M.J. / Parepalo, M. / Meri, S. / Goldman, A.
History
DepositionFeb 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement factor H


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water3,189177
1
A: Complement factor H

A: Complement factor H

A: Complement factor H

A: Complement factor H


Theoretical massNumber of molelcules
Total (without water)57,1894
Polymers57,1894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area7930 Å2
ΔGint-35 kcal/mol
Surface area25450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.410, 91.410, 110.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsCrystal packing of FH19-20 in the asymmetric unit reveals tightly packed tetrameric assembly of domains of FH19-20; may have biological relevance

-
Components

#1: Protein Complement factor H / H factor 1


Mass: 14297.312 Da / Num. of mol.: 1 / Fragment: C-terminal Domains 19-20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1 / Plasmid: pPICZ B expression vector / Production host: Pichia pastoris (fungus) / References: UniProt: P08603
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Before crystallization the protein was concentrated to 10 mg/ml and dialysed into 20 mM Tris, 50 mM NaCl, pH 7.0. The protein was crystallized in sitting drops by mixing 1 ul of protein ...Details: Before crystallization the protein was concentrated to 10 mg/ml and dialysed into 20 mM Tris, 50 mM NaCl, pH 7.0. The protein was crystallized in sitting drops by mixing 1 ul of protein solution at 10 mg/ml with 1 ul of reservoir solution of 2.2 M (NH4)2SO4, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
ROTATING ANODERIGAKU RU30021.54
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 14, 2003
RIGAKU RAXIS IV2IMAGE PLATEOct 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
21.541
ReflectionResolution: 1.75→14.78 Å / Num. all: 22700 / Num. obs: 22700 / % possible obs: 99.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.059
Reflection shellResolution: 1.75→1.795 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.441 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→14.78 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.631 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22479 1239 5.2 %RANDOM
Rwork0.20641 ---
all0.20735 22700 --
obs0.20735 22700 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.593 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.75→14.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 177 1153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221001
X-RAY DIFFRACTIONr_bond_other_d0.0010.02872
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9631358
X-RAY DIFFRACTIONr_angle_other_deg0.89532038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64624.14641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17915163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.057155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021108
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02200
X-RAY DIFFRACTIONr_nbd_refined0.2130.2202
X-RAY DIFFRACTIONr_nbd_other0.1810.2827
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2477
X-RAY DIFFRACTIONr_nbtor_other0.0850.2562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.320.229
X-RAY DIFFRACTIONr_mcbond_it1.4531.5671
X-RAY DIFFRACTIONr_mcbond_other0.3191.5248
X-RAY DIFFRACTIONr_mcangle_it2.0821006
X-RAY DIFFRACTIONr_scbond_it3.5083435
X-RAY DIFFRACTIONr_scangle_it4.8654.5352
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 87 -
Rwork0.279 1642 -
obs--100 %

+
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