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- PDB-6atg: Insights to complement factor H recruitment by the borrelial CspZ... -

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Basic information

Entry
Database: PDB / ID: 6atg
TitleInsights to complement factor H recruitment by the borrelial CspZ protein as revealed by structural analysis
Components
  • Complement regulator-acquiring surface protein 2 (CRASP-2)
  • HCG40889, isoform CRA_b
KeywordsIMMUNE SYSTEM / Complex / immune evasion
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
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1640 / : / Complement regulator-acquiring surface protein 2 / : / Complement Module, domain 1 / Complement Module; domain 1 / 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. ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1640 / : / Complement regulator-acquiring surface protein 2 / : / Complement Module, domain 1 / Complement Module; domain 1 / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ribbon / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
HCG40889, isoform CRA_b / Complement regulator-acquiring surface protein 2 (CRASP-2) / Complement factor H
Similarity search - Component
Biological speciesHomo sapiens (human)
Borrelia burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLiu, A. / Yan, H. / Wu, Y. / Li, Y. / Liu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01DC006917 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R21DC011066 United States
CitationJournal: To Be Published
Title: Insights to complement factor H recruitment by the borrelial CspZ protein as revealed by structural analysis
Authors: Liu, A. / Yan, H. / Wu, Y. / Li, Y. / Liu, J.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HCG40889, isoform CRA_b
B: Complement regulator-acquiring surface protein 2 (CRASP-2)
C: Complement regulator-acquiring surface protein 2 (CRASP-2)
D: HCG40889, isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3756
Polymers63,3264
Non-polymers492
Water11,908661
1
A: HCG40889, isoform CRA_b
B: Complement regulator-acquiring surface protein 2 (CRASP-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6873
Polymers31,6632
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-14 kcal/mol
Surface area13130 Å2
MethodPISA
2
C: Complement regulator-acquiring surface protein 2 (CRASP-2)
D: HCG40889, isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6873
Polymers31,6632
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-10 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.742, 53.772, 116.587
Angle α, β, γ (deg.)90.000, 92.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HCG40889, isoform CRA_b


Mass: 6984.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_40889 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A024R962, UniProt: P08603*PLUS
#2: Protein Complement regulator-acquiring surface protein 2 (CRASP-2)


Mass: 24679.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi B31 (bacteria) / Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: cspZ, BB_H06 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50665
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 200 mM MgCl2, 100mM Tris-HCl (pH 7.8), and 22-24% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→43.7 Å / Num. obs: 53908 / % possible obs: 98 % / Redundancy: 4.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1158 / Net I/σ(I): 6.1
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3570 / CC1/2: 0.914 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UWN, 4CBE

2uwn

4cbe


Resolution: 1.8→39.5 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 1425 3.01 %
Rwork0.1779 45919 -
obs0.1788 47344 93.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.55 Å2 / Biso mean: 21.668 Å2 / Biso min: 7.08 Å2
Refinement stepCycle: final / Resolution: 1.8→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 2 661 5023
Biso mean--23.55 31 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074457
X-RAY DIFFRACTIONf_angle_d0.765998
X-RAY DIFFRACTIONf_chiral_restr0.046653
X-RAY DIFFRACTIONf_plane_restr0.004769
X-RAY DIFFRACTIONf_dihedral_angle_d5.663581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.86430.2411920.21323193328566
1.8643-1.9390.27461120.19683992410482
1.939-2.02720.27091320.20074677480996
2.0272-2.13410.21841700.188148164986100
2.1341-2.26780.25221490.184848705019100
2.2678-2.44290.22581450.180548825027100
2.4429-2.68870.20581440.182548565000100
2.6887-3.07760.20821440.18374861500599
3.0776-3.87690.18591730.1644856502999
3.8769-39.50920.1771640.16564916508098

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