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- PDB-9f7i: Crystal structure of Borrelia burgdorferi B31 CspZ in complex wit... -

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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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 %

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