[English] 日本語
Yorodumi
- PDB-4aye: Structure of a complex between CCPs 6 and 7 of Human Complement F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aye
TitleStructure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria meningitidis FHbp Variant 1 E283AE304A mutant
Components
  • COMPLEMENT FACTOR H
  • FACTOR H BINDING PROTEIN
KeywordsIMMUNE SYSTEM / ANTIGENS / BACTERIAL PROTEINS / VACCINES
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 MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJohnson, S. / Tan, L. / van der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Everett, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. ...Johnson, S. / Tan, L. / van der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Everett, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Borrow, R. / Pickering, M. / Lea, S.M. / Tang, C.M.
CitationJournal: Plos Pathog. / Year: 2012
Title: Design and Evaluation of Meningococcal Vaccines Through Structure-Based Modification of Host and Pathogen Molecules.
Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / ...Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Ufret-Vincenty, R. / Borrow, R. / Pickering, M.C. / Lea, S.M. / Tang, C.M.
History
DepositionJun 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references / Derived calculations / Structure summary
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CE" 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 "DE" 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 "FE" 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.

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,16225
Polymers125,9826
Non-polymers1,17919
Water2,414134
1
A: COMPLEMENT FACTOR H
D: FACTOR H BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4299
Polymers41,9942
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-9.1 kcal/mol
Surface area20690 Å2
MethodPISA
2
B: COMPLEMENT FACTOR H
C: FACTOR H BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4299
Polymers41,9942
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-9.6 kcal/mol
Surface area21090 Å2
MethodPISA
3
E: COMPLEMENT FACTOR H
F: FACTOR H BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3047
Polymers41,9942
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-8.1 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.413, 53.277, 130.084
Angle α, β, γ (deg.)90.00, 117.74, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.49295, -0.10047, 0.86424), (-0.05113, 0.99494, 0.0865), (-0.86856, -0.00155, -0.49559)-29.71382, 1.55429, -84.0762
2given(-0.48553, -0.16025, -0.85941), (-0.23331, 0.97115, -0.04928), (0.84251, 0.17659, -0.50891)-84.65943, -9.69653, -18.37956
3given(-0.45181, -0.05302, 0.89054), (0.04242, 0.99583, 0.08081), (-0.8911, 0.07429, -0.44768)-29.33192, 2.73927, -84.21825
4given(-0.54764, -0.19066, -0.8147), (-0.15214, 0.98015, -0.12711), (0.82277, 0.05434, -0.56577)-83.98991, -9.62747, -18.1512

-
Components

#1: Protein COMPLEMENT FACTOR H / H FACTOR 1


Mass: 14410.275 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) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: P08603
#2: Protein FACTOR H BINDING PROTEIN


Mass: 27583.869 Da / Num. of mol.: 3 / Fragment: RESIDUES 73-320 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS MC58 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: Q9JXV4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.22 Å3/Da / Density % sol: 44 % / 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: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.8→90.05 Å / Num. obs: 26592 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 66.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.7
Reflection shellResolution: 2.8→2.96 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.3 / % possible all: 70.5

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W81

2w81


Resolution: 2.8→57.57 Å / Cor.coef. Fo:Fc: 0.9034 / Cor.coef. Fo:Fc free: 0.8825 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.359
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 1347 5.07 %RANDOM
Rwork0.2068 ---
obs0.2078 26588 93.35 %-
Displacement parametersBiso mean: 46.77 Å2
Baniso -1Baniso -2Baniso -3
1-5.0372 Å20 Å25.1268 Å2
2---10.4244 Å20 Å2
3---5.3872 Å2
Refine analyzeLuzzati coordinate error obs: 0.396 Å
Refinement stepCycle: LAST / Resolution: 2.8→57.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8437 0 76 134 8647
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078710HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0211726HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2994SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes219HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1274HARMONIC5
X-RAY DIFFRACTIONt_it8710HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.26
X-RAY DIFFRACTIONt_other_torsion18.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1087SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9136SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3451 105 5.18 %
Rwork0.2626 1921 -
all0.2669 2026 -
obs--93.35 %

+
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://pdbjlvh1.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