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- PDB-4ayd: Structure of a complex between CCPs 6 and 7 of Human Complement F... -

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Basic information

Entry
Database: PDB / ID: 4ayd
TitleStructure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria meningitidis FHbp Variant 1 R106A mutant
Components
  • COMPLEMENT FACTOR H
  • FACTOR H BINDING PROTEIN
KeywordsIMMUNE SYSTEM / ANTIGENS / VACCINES
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / bacterial extracellular vesicle / 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 activation, alternative pathway / bacterial extracellular vesicle / 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 / 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: 2.4 Å
AuthorsJohnson, S. / Tan, L. / van der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Everett, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. ...Johnson, S. / Tan, L. / van der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Everett, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Borrow, R. / Pickering, M. / Lea, S.M. / Tang, C.M.
CitationJournal: Plos Pathog. / Year: 2012
Title: Design and Evaluation of Meningococcal Vaccines Through Structure-Based Modification of Host and Pathogen Molecules
Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / ...Authors: Johnson, S. / Tan, L. / Van Der Veen, S. / Caesar, J. / Goicoechea De Jorge, E. / Harding, R.J. / Bai, X. / Exley, R.M. / Ward, P.N. / Ruivo, N. / Trivedi, K. / Cumber, E. / Jones, R. / Newham, L. / Staunton, D. / Ufret-Vincenty, R. / Borrow, R. / Pickering, M. / Lea, S.M. / Tang, C.M.
History
DepositionJun 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 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 "FB" 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.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,32110
Polymers126,0726
Non-polymers2484
Water14,880826
1
A: COMPLEMENT FACTOR H
D: FACTOR H BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0863
Polymers42,0242
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-2.1 kcal/mol
Surface area17460 Å2
MethodPISA
2
B: COMPLEMENT FACTOR H
C: FACTOR H BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0863
Polymers42,0242
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-3.4 kcal/mol
Surface area17500 Å2
MethodPISA
3
E: COMPLEMENT FACTOR H
F: FACTOR H BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1484
Polymers42,0242
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-2.4 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.260, 54.010, 129.560
Angle α, β, γ (deg.)90.00, 118.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.488862, 0.100011, 0.86661), (0.033451, 0.994825, -0.095937), (-0.87172, -0.017911, -0.489677)-0.24135, -0.01446, -0.4905
2given(-0.48518, 0.157, -0.86021), (0.22583, 0.97287, 0.05019), (0.84475, -0.1699, -0.50747)-0.3573, 0.14319, -0.1327
3given(-0.45858, 0.09482, 0.88358), (-0.0121, 0.99353, -0.11291), (-0.88857, -0.06247, -0.45447)-0.22376, -0.06491, -0.48181
4given(-0.55281, 0.17237, -0.81529), (0.16321, 0.98182, 0.09692), (0.81717, -0.07949, -0.57089)-0.38442, 0.12996, -0.18228

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Components

#1: Protein COMPLEMENT FACTOR H / H FACTOR 1


Mass: 14410.275 Da / Num. of mol.: 3 / Fragment: CCPS 6 AND 7, RESIDUES 321-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: HIS402 POLYMORPHISM / Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P08603
#2: Protein FACTOR H BINDING PROTEIN


Mass: 27613.822 Da / Num. of mol.: 3 / Fragment: RESIDUES 73-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Strain: MC58 / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9JXV4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN C, ARG 106 TO ALA ENGINEERED RESIDUE IN CHAIN D, ARG 106 TO ALA ...ENGINEERED RESIDUE IN CHAIN C, ARG 106 TO ALA ENGINEERED RESIDUE IN CHAIN D, ARG 106 TO ALA ENGINEERED RESIDUE IN CHAIN F, ARG 106 TO ALA
Has protein modificationY
Sequence detailsTHIS IS THE HIS402 POLYMORPHISM. MG AT THE START COME FROM THE VECTOR. N AND C-TERMINAL RESIDUE ...THIS IS THE HIS402 POLYMORPHISM. MG AT THE START COME FROM THE VECTOR. N AND C-TERMINAL RESIDUE DISCREPANCIES ARE FROM THE VECTOR

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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: 2.22 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 9 / Details: 20% PEG 6000, 0.1M BICINE PH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97264
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97264 Å / Relative weight: 1
ReflectionResolution: 2.4→114.4 Å / Num. obs: 43520 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 51.98 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 86.1

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W81

2w81


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.9188 / Cor.coef. Fo:Fc free: 0.9026 / SU R Cruickshank DPI: 0.589 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.76 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.258
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 2199 5.08 %RANDOM
Rwork0.2023 ---
obs0.2038 43305 97.09 %-
Displacement parametersBiso mean: 40.53 Å2
Baniso -1Baniso -2Baniso -3
1-8.1588 Å20 Å22.3431 Å2
2---11.2942 Å20 Å2
3---3.1354 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8386 0 16 826 9228
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078606HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9911612HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2959SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes224HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1259HARMONIC5
X-RAY DIFFRACTIONt_it8606HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion17.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1081SEMIHARMONIC5
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_contact9716SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2867 156 5.74 %
Rwork0.2428 2560 -
all0.2452 2716 -
obs--97.09 %

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