[English] 日本語
Yorodumi
- PDB-2w81: Structure of a complex between Neisseria meningitidis factor H bi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w81
TitleStructure of a complex between Neisseria meningitidis factor H binding protein and CCPs 6-7 of human complement factor H
Components
  • COMPLEMENT FACTOR HFactor H
  • FACTOR H BINDING PROTEIN
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / IMMUNE EVASION / AGE-RELATED MACULAR DEGENERATION / INNATE IMMUNITY / IMMUNE RESPONSE / DISEASE MUTATION / FACTOR H / COMPLEMENT ALTERNATE PATHWAY / VACCINE CANDIDATE
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / bacterial extracellular vesicle / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation ...regulation of complement activation, alternative pathway / bacterial extracellular vesicle / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / cell outer membrane / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Immunoglobulin-like - #1980 / : / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Porin - #90 / Complement Module, domain 1 / Complement Module; domain 1 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel ...Immunoglobulin-like - #1980 / : / : / Factor H binding protein, N-terminal / Factor H binding protein, C-terminal / Factor H binding protein, C-terminal / Porin - #90 / Complement Module, domain 1 / Complement Module; domain 1 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Complement factor H / Factor H binding protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
NEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSchneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. ...Schneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. / Roversi, P. / Johnson, S. / Tang, C.M. / Lea, S.M.
CitationJournal: Nature / Year: 2009
Title: Neisseria Meningitidis Recruits Factor H Using Protein Mimicry of Host Carbohydrates.
Authors: Schneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. / Roversi, P. / Johnson, S. / Tang, C.M. / Lea, S.M.
History
DepositionJan 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COMPLEMENT FACTOR H
B: COMPLEMENT FACTOR H
C: FACTOR H BINDING PROTEIN
D: FACTOR H BINDING PROTEIN
E: COMPLEMENT FACTOR H
F: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)123,6156
Polymers123,6156
Non-polymers00
Water7,638424
1
A: COMPLEMENT FACTOR H
D: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,2052
Polymers41,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-4.44 kcal/mol
Surface area17090 Å2
MethodPISA
2
B: COMPLEMENT FACTOR H
C: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,2052
Polymers41,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-5.95 kcal/mol
Surface area17270 Å2
MethodPISA
3
E: COMPLEMENT FACTOR H
F: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,2052
Polymers41,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-6.2 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.520, 52.210, 128.780
Angle α, β, γ (deg.)90.00, 118.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2050-

HOH

21E-2039-

HOH

-
Components

#1: Protein COMPLEMENT FACTOR H / Factor H / H FACTOR 1


Mass: 14222.026 Da / Num. of mol.: 3 / Fragment: CCPS 6 AND 7, RESIDUES 321-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Variant: HIS 402 FORM / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08603
#2: Protein FACTOR H BINDING PROTEIN


Mass: 26983.078 Da / Num. of mol.: 3
Fragment: FULL PROTEIN WITHOUT SIGNAL SEQUENCE, RESIDUES 71-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JXV4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFRAGMENT OF THIS ENTRY -CCPS 6 AND 7 ONLY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.21 % / Description: NONE
Crystal growpH: 9 / Details: 20% PEG 6000, 0.1M BICINE PH 9.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9814
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 43159 / % possible obs: 94.3 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 46.43 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
SOLOMONmodel building
xia2WITH XDSdata reduction
xia2WITH SCALAdata scaling
BUSTER-TNTphasing
PHASERphasing
SHARPphasing
SOLOMONphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UWN

2uwn


Resolution: 2.35→38.81 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE 3 COPIES OF THE COMPLEX IN THE ASYMMETRIC UNIT, BUT SUBTLE REARRANGMENTS MEAN THAT NCS WAS NOT USED IN THE FINAL REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2187 5.08 %RANDOM
Rwork0.274 ---
obs0.275 43084 93.8 %-
Displacement parametersBiso mean: 42.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.30662 Å20 Å22.57021 Å2
2---11.03004 Å20 Å2
3---10.72342 Å2
Refinement stepCycle: LAST / Resolution: 2.35→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8412 0 0 424 8836
LS refinement shellResolution: 2.35→2.49 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3434 368 5.33 %
Rwork0.3102 6538 -
all0.312 6906 -
obs--93.84 %

+
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