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- PDB-2g7i: Structure of Human Complement Factor H Carboxyl Terminal Domains ... -

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Basic information

Entry
Database: PDB / ID: 2g7i
TitleStructure of Human Complement Factor H Carboxyl Terminal Domains 19-20: a Basis for Atypical Hemolytic Uremic Syndrome
ComponentsComplement factor HFactor H
KeywordsIMMUNE SYSTEM / Sushi (CCP/SCR) domain / Complement / Regulator / Factor H / Beta-1H Globulin / Atypical Hemolytic Uremic Syndrome / Heparin Binding
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / Regulation of Complement cascade ...regulation of complement activation, alternative pathway / symbiont cell surface / complement component C3b binding / regulation of complement-dependent cytotoxicity / regulation of complement activation / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / 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 / SAD / Resolution: 1.75 Å
AuthorsJaakola, V.-P. / Jokiranta, T.S. / Goldman, A.
CitationJournal: Embo J. / Year: 2006
Title: Structure of complement factor H carboxyl-terminus reveals molecular basis of atypical haemolytic uremic syndrome.
Authors: Jokiranta, T.S. / Jaakola, V.-P. / Lehtinen, M.J. / Parepalo, M. / Meri, S. / Goldman, A.
History
DepositionFeb 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement factor H


Theoretical massNumber of molelcules
Total (without water)14,2971
Polymers14,2971
Non-polymers00
Water3,189177
1
A: Complement factor H

A: Complement factor H

A: Complement factor H

A: Complement factor H


Theoretical massNumber of molelcules
Total (without water)57,1894
Polymers57,1894
Non-polymers00
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 area7930 Å2
ΔGint-35 kcal/mol
Surface area25450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.410, 91.410, 110.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsCrystal packing of FH19-20 in the asymmetric unit reveals tightly packed tetrameric assembly of domains of FH19-20; may have biological relevance

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Components

#1: Protein Complement factor H / Factor H / H factor 1


Mass: 14297.312 Da / Num. of mol.: 1 / Fragment: C-terminal Domains 19-20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFH, HF, HF1 / Plasmid: pPICZ B expression vector / Production host: Pichia pastoris (fungus) / References: UniProt: P08603
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Before crystallization the protein was concentrated to 10 mg/ml and dialysed into 20 mM Tris, 50 mM NaCl, pH 7.0. The protein was crystallized in sitting drops by mixing 1 ul of protein ...Details: Before crystallization the protein was concentrated to 10 mg/ml and dialysed into 20 mM Tris, 50 mM NaCl, pH 7.0. The protein was crystallized in sitting drops by mixing 1 ul of protein solution at 10 mg/ml with 1 ul of reservoir solution of 2.2 M (NH4)2SO4, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
ROTATING ANODERIGAKU RU30021.54
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 14, 2003
RIGAKU RAXIS IV2IMAGE PLATEOct 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
21.541
ReflectionResolution: 1.75→14.78 Å / Num. all: 22700 / Num. obs: 22700 / % possible obs: 99.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.059
Reflection shellResolution: 1.75→1.795 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.441 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→14.78 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.631 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22479 1239 5.2 %RANDOM
Rwork0.20641 ---
all0.20735 22700 --
obs0.20735 22700 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.593 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.75→14.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 177 1153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221001
X-RAY DIFFRACTIONr_bond_other_d0.0010.02872
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9631358
X-RAY DIFFRACTIONr_angle_other_deg0.89532038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64624.14641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17915163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.057155
X-RAY DIFFRACTIONr_chiral_restr0.1180.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021108
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02200
X-RAY DIFFRACTIONr_nbd_refined0.2130.2202
X-RAY DIFFRACTIONr_nbd_other0.1810.2827
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2477
X-RAY DIFFRACTIONr_nbtor_other0.0850.2562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.320.229
X-RAY DIFFRACTIONr_mcbond_it1.4531.5671
X-RAY DIFFRACTIONr_mcbond_other0.3191.5248
X-RAY DIFFRACTIONr_mcangle_it2.0821006
X-RAY DIFFRACTIONr_scbond_it3.5083435
X-RAY DIFFRACTIONr_scangle_it4.8654.5352
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 87 -
Rwork0.279 1642 -
obs--100 %

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