[English] 日本語
Yorodumi
- PDB-6zh1: Crystal structure of complex between FH19-20 and FhbA protein fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zh1
TitleCrystal structure of complex between FH19-20 and FhbA protein from Borrelia hermsii
Components
  • Complement factor HFactor H
  • Factor H-binding protein A
KeywordsIMMUNE SYSTEM / Innate immunity / complement / relapsing fever / Lyme disease
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / 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 ...regulation of complement activation, alternative pathway / 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 / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
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
Similarity search - Domain/homology
Complement factor H / Uncharacterized protein
Similarity search - Component
Biological speciesBorrelia hermsii YOR (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKogan, K. / Kotila, T. / Meri, T. / Goldman, A.
Funding support Finland, United Kingdom, 2items
OrganizationGrant numberCountry
Sigrid Juselius FoundationBBSRC 104399 Finland
Wellcome Trust478571 United Kingdom
CitationJournal: Plos Pathog. / Year: 2022
Title: Mechanism of Borrelia immune evasion by FhbA-related proteins.
Authors: Kogan, K. / Haapasalo, K. / Kotila, T. / Moore, R. / Lappalainen, P. / Goldman, A. / Meri, T.
History
DepositionJun 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Factor H-binding protein A
B: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,96211
Polymers37,2332
Non-polymers7299
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Two proteins elute as one peak in PBS and also in PBS + 500mM NaCl., assay for oligomerization, Microscale thermophoresis and radioactive-labeled ligand binding studies
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-46 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.273, 60.327, 145.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Factor H-binding protein A / Factor H-binding protein A


Mass: 22148.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Factor H-binding protein A / Source: (gene. exp.) Borrelia hermsii YOR (bacteria) / Gene: BHY_1174 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W5SB08
#2: Protein Complement factor H / Factor H / H factor 1


Mass: 15084.103 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1, HF2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P08603
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1 M MES pH6.7, 0.2 M Ammonium Sulfate, 20% (v/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.2→37.828 Å / Num. obs: 20180 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 49.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.047 / Rrim(I) all: 0.172 / Net I/av σ(I): 12.531 / Net I/σ(I): 12.531
Reflection shellResolution: 2.2→2.237 Å / Redundancy: 13.78 % / Rmerge(I) obs: 2.436 / Mean I/σ(I) obs: 1 / Num. unique obs: 993 / CC1/2: 0.513 / Rpim(I) all: 0.673 / Rrim(I) all: 2.529 / % possible all: 99

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
autoPROC10.10.5data scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G7I

2g7i


Resolution: 2.2→22.88 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.187
RfactorNum. reflection% reflectionSelection details
Rfree0.24 984 4.89 %RANDOM
Rwork0.19 ---
obs0.193 20103 99.9 %-
Displacement parametersBiso max: 160.42 Å2 / Biso mean: 59.9 Å2 / Biso min: 27.31 Å2
Baniso -1Baniso -2Baniso -3
1-7.8029 Å20 Å20 Å2
2---16.9576 Å20 Å2
3---9.1546 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.2→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 41 154 2532
Biso mean--100.7 61.52 -
Num. residues----285
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d884SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes407HARMONIC5
X-RAY DIFFRACTIONt_it2430HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion303SEMIHARMONIC5
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_contact2809SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2430HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3270HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion16.86
LS refinement shellResolution: 2.2→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2722 138 4.78 %
Rwork0.2492 2747 -
all0.2504 2885 -
obs--99.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.56130.25270.46611.03130.65271.92150.13881.2933-0.9445-0.40480.01730.19530.7623-0.0604-0.15610.6258-0.0343-0.29321.1038-0.84080.45470.9442-23.886513.4458
20.84550.36231.05310.8511-0.35352.55970.30810.2285-0.0793-0.62950.38790.03831.3151-0.2654-0.6960.709-0.3232-0.33090.29490.1647-0.2947-14.5047-8.87924.5587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A44 - 202
2X-RAY DIFFRACTION2{ B|* }B1106 - 1231

+
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