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- PDB-2w80: Structure of a complex between Neisseria meningitidis factor H bi... -

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Basic information

Entry
Database: PDB / ID: 2w80
TitleStructure of a complex between Neisseria meningitidis factor H binding protein and CCPs 6-7 of human complement factor H
Components
  • COMPLEMENT FACTOR H
  • FACTOR H BINDING PROTEIN
KeywordsIMMUNE SYSTEM / GLYCOPROTEIN / IMMUNE EVASION / AGE-RELATED MACULAR DEGENERATION / INNATE IMMUNITY / IMMUNE RESPONSE / DISEASE MUTATION / FACTOR H / COMPLEMENT ALTERNATE PATHWAY / VACCINE CANDIDATE
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / bacterial extracellular vesicle / 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 activation, alternative pathway / bacterial extracellular vesicle / 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 / 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, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Porin - #90 / : / Complement Module, domain 1 / Complement Module; domain 1 ...Immunoglobulin-like - #1980 / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-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. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Complement factor H / Factor H binding protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
NEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSchneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. ...Schneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. / Roversi, P. / Johnson, S. / Tang, C.M. / Lea, S.M.
CitationJournal: Nature / Year: 2009
Title: Neisseria Meningitidis Recruits Factor H Using Protein Mimicry of Host Carbohydrates.
Authors: Schneider, M.C. / Prosser, B.E. / Caesar, J.J.E. / Kugelberg, E. / Li, S. / Zhang, Q. / Quoraishi, S. / Lovett, J.E. / Deane, J.E. / Sim, R.B. / Roversi, P. / Johnson, S. / Tang, C.M. / Lea, S.M.
History
DepositionJan 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CC" 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 "DC" 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 "FC" 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 "HC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
G: COMPLEMENT FACTOR H
H: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)164,8208
Polymers164,8208
Non-polymers00
Water9,152508
1
A: COMPLEMENT FACTOR H
D: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,2052
Polymers41,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-6.43 kcal/mol
Surface area17440 Å2
MethodPISA
2
B: COMPLEMENT FACTOR H
C: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,2052
Polymers41,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-6.72 kcal/mol
Surface area17220 Å2
MethodPISA
3
E: COMPLEMENT FACTOR H
F: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,2052
Polymers41,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-7.31 kcal/mol
Surface area17260 Å2
MethodPISA
4
G: COMPLEMENT FACTOR H
H: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,2052
Polymers41,2052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-5.49 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.704, 93.847, 99.720
Angle α, β, γ (deg.)80.07, 80.18, 84.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
COMPLEMENT FACTOR H / H FACTOR 1


Mass: 14222.026 Da / Num. of mol.: 4 / Fragment: CCPS 6 AND 7, RESIDUES 321-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Variant: HIS 402 FORM / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08603
#2: Protein
FACTOR H BINDING PROTEIN


Mass: 26983.078 Da / Num. of mol.: 4
Fragment: FULL PROTEIN WITHOUT SIGNAL SEQUENCE, RESIDUES 71-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JXV4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFRAGMENT OF THIS ENTRY -CCPS 6 AND 7 ONLY

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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: 2.64 Å3/Da / Density % sol: 53.06 % / Description: NONE
Crystal growpH: 9 / Details: 20% PEG 6000, 0.1M BICINE PH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9523
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9523 Å / Relative weight: 1
ReflectionResolution: 2.35→95 Å / Num. obs: 64754 / % possible obs: 91.3 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 50.27 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.1 / % possible all: 80.9

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Processing

Software
NameVersionClassification
SOLOMONmodel building
xia2WITH XDSdata reduction
xia2WITH SCALAdata scaling
BUSTER-TNTphasing
PHASERphasing
SHARPphasing
SOLOMONphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UWN

2uwn


Resolution: 2.35→95 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE 4 COPIES OF THE COMPLEX IN THE ASYMMETRIC UNIT, BUT SUBTLE REARRANGMENTS MEAN THAT NCS WAS NOT USED IN THE FINAL REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3312 5.05 %RANDOM
Rwork0.233 ---
obs0.234 65520 91.8 %-
Displacement parametersBiso mean: 40.61 Å2
Baniso -1Baniso -2Baniso -3
1--8.1839 Å2-18.09152 Å22.83322 Å2
2---2.09226 Å2-1.53111 Å2
3---10.27615 Å2
Refinement stepCycle: LAST / Resolution: 2.35→95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11379 0 0 508 11887
LS refinement shellResolution: 2.35→2.49 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3411 496 4.9 %
Rwork0.2888 9628 -
all0.2914 10124 -
obs--91.82 %

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