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

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Basic information

Entry
Database: PDB / ID: 4aym
TitleStructure of a complex between CCPs 6 and 7 of Human Complement Factor H and Neisseria meningitidis FHbp Variant 3 P106A 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 / 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 ...regulation of complement activation, alternative pathway / 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 / Lipoprotein GNA1870
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
NEISSERIA MENINGITIDIS MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / Other ...Database references / Other / Source and taxonomy / Structure summary
Revision 1.3Dec 20, 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 16, 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 "CB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" 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 "DB" 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: COMPLEMENT FACTOR H


Theoretical massNumber of molelcules
Total (without water)116,6176
Polymers116,6176
Non-polymers00
Water1086
1
B: COMPLEMENT FACTOR H
C: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)43,8982
Polymers43,8982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-14 kcal/mol
Surface area16880 Å2
MethodPISA
2
A: COMPLEMENT FACTOR H
D: FACTOR H BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)43,8982
Polymers43,8982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-12.8 kcal/mol
Surface area16810 Å2
MethodPISA
3
E: COMPLEMENT FACTOR H


Theoretical massNumber of molelcules
Total (without water)14,4101
Polymers14,4101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
F: COMPLEMENT FACTOR H


Theoretical massNumber of molelcules
Total (without water)14,4101
Polymers14,4101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.090, 83.490, 361.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.06418, -0.99791, -0.00814), (-0.99767, 0.06397, 0.02379), (-0.02322, 0.00965, -0.99968)36.81477, -3.23296, -90.16554
2given(-0.97337, -0.11097, -0.20059), (0.19249, -0.87086, -0.45228), (-0.1245, -0.47885, 0.86903)32.17978, -8.52439, -39.80519
3given(-0.18391, 0.85896, 0.47787), (0.97959, 0.12005, 0.16121), (0.0811, 0.49777, -0.86351)44.12083, -37.01143, -49.90411
4given(-0.08817, -0.99599, -0.01507), (-0.99581, 0.08776, 0.02565), (-0.02422, 0.01727, -0.99956)36.69062, -2.95715, -90.17303

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Components

#1: Protein
COMPLEMENT FACTOR H / H FACTOR 1


Mass: 14410.275 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: 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 FACTOR H BINDING PROTEIN / LIPOPROTEIN GNA1870


Mass: 29487.807 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-281 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS MC58 (bacteria) / Variant: P28 / Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B / Variant (production host): B834(DE3) / References: UniProt: Q19KF7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN C, PRO 65 TO ALA ENGINEERED RESIDUE IN CHAIN D, PRO 65 TO ALA
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). PRO106 HAS BEEN MUTATED TO ALA.

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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: 2.53 Å3/Da / Density % sol: 51 % / 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: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→180 Å / Num. obs: 28212 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 73.84 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.6
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5

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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: 3→15 Å / Cor.coef. Fo:Fc: 0.8502 / Cor.coef. Fo:Fc free: 0.8691 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.418
Details: NUMBER OF RESTRAINT LIBRARIES USED: 7 REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1213 5.06 %RANDOM
Rwork0.2543 ---
obs0.2545 23962 99.94 %-
Displacement parametersBiso mean: 56.74 Å2
Baniso -1Baniso -2Baniso -3
1--7.6877 Å20 Å20 Å2
2---7.6777 Å20 Å2
3---15.3654 Å2
Refine analyzeLuzzati coordinate error obs: 0.538 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7500 0 0 6 7506
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077723HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0710465HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2591SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes192HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1124HARMONIC5
X-RAY DIFFRACTIONt_it7723HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion17.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion962SEMIHARMONIC5
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_contact7849SEMIHARMONIC4
LS refinement shellResolution: 3→3.13 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3136 162 5.63 %
Rwork0.2805 2715 -
all0.2824 2877 -
obs--99.94 %

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