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- PDB-3kxv: Structure of complement Factor H variant Q1139A -

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Basic information

Entry
Database: PDB / ID: 3kxv
TitleStructure of complement Factor H variant Q1139A
ComponentsComplement factor H
KeywordsIMMUNE SYSTEM / Sushi domain / short consensus repeat domain / SCR domain / complement control protein module / complement regulator / atypical hemolytic uremic syndrome / renal disease / CFH / complement alternative pathway / disease mutation / glycoprotein / immune response / innate immunity
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 / heparin binding / blood microparticle / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
: / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsBhattacharjee, A. / Lehtinen, M.J. / Kajander, T. / Goldman, A. / Jokiranta, T.S.
CitationJournal: Mol.Immunol. / Year: 2010
Title: Both domain 19 and domain 20 of factor H are involved in binding to complement C3b and C3d
Authors: Bhattacharjee, A. / Lehtinen, M.J. / Kajander, T. / Goldman, A. / Jokiranta, T.S.
History
DepositionDec 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6197
Polymers15,0421
Non-polymers5766
Water2,036113
1
A: Complement factor H
hetero molecules

A: Complement factor H
hetero molecules

A: Complement factor H
hetero molecules

A: Complement factor H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,47428
Polymers60,1694
Non-polymers2,30624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area7880 Å2
ΔGint-38 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.460, 91.460, 110.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Complement factor H / H factor 1


Mass: 15042.128 Da / Num. of mol.: 1 / Fragment: Sushi domains 19-20 / Mutation: Q1139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPICZ-alpha- B / Production host: Pichia pastoris (fungus) / References: UniProt: P08603
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2M ammonium sulphate, 0.1M Bis-Tris buffer, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16014 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.116 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.097 / Net I/σ(I): 16.8
Reflection shellResolution: 2→2.13 Å / Redundancy: 7.16 % / Mean I/σ(I) obs: 3.43 / Num. unique all: 18145 / Rsym value: 0.552 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G7I

2g7i


Resolution: 2.004→42.012 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.844 / SU ML: 1.86
Isotropic thermal model: Isotropic individual temperature factors
Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.27 / Stereochemistry target values: ML / Details: The structure was refined also with REFMAC 5.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 804 5 %Random
Rwork0.2067 ---
all0.2086 ---
obs0.2086 15271 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.504 Å2 / ksol: 0.403 e/Å3
Displacement parametersBiso max: 82.04 Å2 / Biso mean: 25.159 Å2 / Biso min: 11.39 Å2
Baniso -1Baniso -2Baniso -3
1-2.707 Å20 Å2-0 Å2
2--2.707 Å20 Å2
3----5.414 Å2
Refinement stepCycle: LAST / Resolution: 2.004→42.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 30 113 1116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061041
X-RAY DIFFRACTIONf_angle_d1.0261417
X-RAY DIFFRACTIONf_dihedral_angle_d16.789368
X-RAY DIFFRACTIONf_chiral_restr0.077147
X-RAY DIFFRACTIONf_plane_restr0.004177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.0041-2.12960.24841310.20842495
2.1296-2.2940.25321320.20452500
2.294-2.52490.22981320.20992504
2.5249-2.89020.24791330.21772531
2.8902-3.6410.26481350.20532562
3.641-42.02130.22491410.19522677

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