[English] 日本語
Yorodumi
- PDB-9f7i: Crystal structure of Borrelia burgdorferi B31 CspZ in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f7i
TitleCrystal structure of Borrelia burgdorferi B31 CspZ in complex with human FH SCR6-7
Components
  • Complement factor H
  • Complement regulator-acquiring surface protein 2 (CRASP-2)
KeywordsIMMUNE SYSTEM / complement-binding protein / Lyme disease / borreliosis
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / regulation of complement-dependent cytotoxicity / complement component C3b binding / regulation of complement activation / 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 / complement component C3b binding / regulation of complement activation / 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 / metal ion binding / identical protein binding
Similarity search - Function
: / Complement regulator-acquiring surface protein 2 / : / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Complement regulator-acquiring surface protein 2 (CRASP-2) / Complement factor H
Similarity search - Component
Biological speciesBorreliella burgdorferi B31 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBrangulis, K. / Surth, V. / Marcinkiewicz, A.L. / Akopjana, I. / Kazaks, A. / Bogans, J. / Huber, A. / Lin, Y.-P. / Kraiczy, P.
Funding support1items
OrganizationGrant numberCountry
Other governmentlzp-2021/1-0068
CitationJournal: To Be Published
Title: Crystal structure of Borrelia burgdorferi B31 CspZ in complex with human FH SCR6-7
Authors: Brangulis, K. / Surth, V. / Marcinkiewicz, A.L. / Akopjana, I. / Kazaks, A. / Bogans, J. / Huber, A. / Lin, Y.-P. / Kraiczy, P.
History
DepositionMay 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement regulator-acquiring surface protein 2 (CRASP-2)
B: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6895
Polymers39,4322
Non-polymers2583
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.661, 67.095, 143.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Complement regulator-acquiring surface protein 2 (CRASP-2)


Mass: 25052.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Strain: B31 / Gene: cspZ, BB_H06 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50665
#2: Protein Complement factor H / H factor 1 / Complement inhibitor factor H SCR domains 6-7


Mass: 14379.221 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.25 M ammonium sulfate 0.1 M MES pH 6.5 10% PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.85→49.07 Å / Num. obs: 11213 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.153 / Net I/σ(I): 11.1
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1580 / CC1/2: 0.939 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→49.07 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.352 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26062 523 4.9 %RANDOM
Rwork0.20086 ---
obs0.20402 10111 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.85→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 11 62 2743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132747
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162541
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.6453707
X-RAY DIFFRACTIONr_angle_other_deg1.2741.5885877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4735328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13923.586145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72915484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1871511
X-RAY DIFFRACTIONr_chiral_restr0.0740.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.135.0421321
X-RAY DIFFRACTIONr_mcbond_other4.1325.0431320
X-RAY DIFFRACTIONr_mcangle_it6.3397.5511646
X-RAY DIFFRACTIONr_mcangle_other6.3377.5491647
X-RAY DIFFRACTIONr_scbond_it4.6475.5151425
X-RAY DIFFRACTIONr_scbond_other4.5275.4821415
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0528.0442044
X-RAY DIFFRACTIONr_long_range_B_refined10.10458.0973113
X-RAY DIFFRACTIONr_long_range_B_other10.10658.0823112
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 37 -
Rwork0.246 733 -
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