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

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Basic information

Entry
Database: PDB / ID: 4ayi
TitleStructure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria meningitidis FHbp Variant 3 Wild type
Components
  • COMPLEMENT FACTOR H
  • LIPOPROTEIN GNA1870 CCOMPND 7
KeywordsIMMUNE SYSTEM / ANTIGENS
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 / 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 / Lipoprotein GNA1870
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
NEISSERIA MENINGITIDIS MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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.C. / Lea, S.M. / Tang, C.M.
History
DepositionJun 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references / Derived calculations
Revision 1.2Mar 25, 2015Group: Database references / Source and taxonomy / Structure summary
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 1.4Oct 23, 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 "DC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT FACTOR H
D: LIPOPROTEIN GNA1870 CCOMPND 7
E: COMPLEMENT FACTOR H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3964
Polymers58,3343
Non-polymers621
Water3,675204
1
A: COMPLEMENT FACTOR H
D: LIPOPROTEIN GNA1870 CCOMPND 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9863
Polymers43,9242
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-10 kcal/mol
Surface area16840 Å2
MethodPISA
2
E: COMPLEMENT FACTOR H


Theoretical massNumber of molelcules
Total (without water)14,4101
Polymers14,4101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.130, 57.130, 363.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.88845, 0.10024, -0.44789), (-0.22165, -0.94823, 0.22746), (-0.4019, 0.30136, 0.86467)
Vector: -21.24986, -33.24406, 40.27188)

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Components

#1: Protein COMPLEMENT FACTOR H / H FACTOR 1


Mass: 14410.275 Da / Num. of mol.: 2 / Fragment: CCPS 6 AND 7, RESIDUES 321-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Variant: HIS402 POLYMORPHISM / Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): B834(DE3) / References: UniProt: P08603
#2: Protein LIPOPROTEIN GNA1870 CCOMPND 7 / FACTOR H BINDING PROTEIN


Mass: 29513.842 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS MC58 (bacteria) / Variant: P28 / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): B834(DE3) / References: UniProt: Q19KF7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS IS THE HIS402 POLYMORPHISM. MG AT THE START COME FROM THE VECTOR. DISCREPANCIES AT TERMINII ...THIS IS THE HIS402 POLYMORPHISM. MG AT THE START COME FROM THE VECTOR. DISCREPANCIES AT TERMINII ARE FROM VECTOR. THE SEQUENCE HAS BEEN RENUMBERED TO MATCH THAT OF THE VARIANT 1 SEQUENCE (PDBID 2W81)

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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: 2.54 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 6 / Details: 0.2 M IMIDAZOLE PH 6 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97932
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.31→57.1 Å / Num. obs: 27284 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Biso Wilson estimate: 58.87 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.5
Reflection shellResolution: 2.31→2.38 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.6 / % possible all: 98.6

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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: 2.31→15 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.9013 / SU R Cruickshank DPI: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.331 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.225
Details: NUMBER OF RESRAINT LIBRARIES USED : 8 IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1362 5.02 %RANDOM
Rwork0.2157 ---
obs0.2175 27148 98.09 %-
Displacement parametersBiso mean: 54.92 Å2
Baniso -1Baniso -2Baniso -3
1--7.8118 Å20 Å20 Å2
2---7.8118 Å20 Å2
3---15.6235 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: LAST / Resolution: 2.31→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 4 204 4013
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083923HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075317HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1316SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes571HARMONIC5
X-RAY DIFFRACTIONt_it3923HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion19.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion488SEMIHARMONIC5
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_contact4292SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.4 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2934 125 4.79 %
Rwork0.2623 2486 -
all0.2639 2611 -
obs--98.09 %

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