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- PDB-4muc: The 4th and 5th C-terminal domains of Factor H related protein 1 -

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Basic information

Entry
Database: PDB / ID: 4muc
TitleThe 4th and 5th C-terminal domains of Factor H related protein 1
ComponentsComplement factor H-related protein 1
KeywordsIMMUNE SYSTEM / Sushi domains / Complement Alternative Pathway / Factor H related proteins
Function / homology
Function and homology information


complement component C3b binding / complement activation / cytolysis by host of symbiont cells / negative regulation of protein binding / Regulation of Complement cascade / blood microparticle / protein-containing complex / extracellular space / 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
Complement factor H-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.897 Å
AuthorsBhattacharjee, A. / Goldman, A. / Kolodziejczyk, R. / Jokiranta, T.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Major Autoantibody Epitope on Factor H in Atypical Hemolytic Uremic Syndrome Is Structurally Different from Its Homologous Site in Factor H-related Protein 1, Supporting a Novel Model for ...Title: The Major Autoantibody Epitope on Factor H in Atypical Hemolytic Uremic Syndrome Is Structurally Different from Its Homologous Site in Factor H-related Protein 1, Supporting a Novel Model for Induction of Autoimmunity in This Disease.
Authors: Bhattacharjee, A. / Reuter, S. / Trojnar, E. / Kolodziejczyk, R. / Seeberger, H. / Hyvarinen, S. / Uzonyi, B. / Szilagyi, A. / Prohaszka, Z. / Goldman, A. / Jozsi, M. / Jokiranta, T.S.
History
DepositionSep 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement factor H-related protein 1
B: Complement factor H-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1519
Polymers28,4782
Non-polymers6727
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-111 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.406, 143.406, 77.784
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Complement factor H-related protein 1 / FHR-1 / H factor-like protein 1 / H-factor-like 1 / H36


Mass: 14239.248 Da / Num. of mol.: 2 / Fragment: Sushi domains 4 and 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFHR1, CFHL, CFHL1, CFHL1P, CFHR1P, FHR1, HFL1, HFL2 / Production host: Pichia pastoris (fungus) / References: UniProt: Q03591
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
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: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2 M ammonium sulphate and 0.1 M sodium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2012
RadiationMonochromator: ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 10935 / % possible obs: 12.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.897→3.07 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DNAdata collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.897→48.529 Å / SU ML: 0.41 / σ(F): 2 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2686 1092 10 %RANDOM
Rwork0.207 ---
obs0.2132 10921 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.897→48.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 35 0 1939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091989
X-RAY DIFFRACTIONf_angle_d1.1622703
X-RAY DIFFRACTIONf_dihedral_angle_d15.733714
X-RAY DIFFRACTIONf_chiral_restr0.067290
X-RAY DIFFRACTIONf_plane_restr0.005345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8972-3.0290.37081320.30311184X-RAY DIFFRACTION98
3.029-3.18870.33351330.29091198X-RAY DIFFRACTION100
3.1887-3.38840.31251320.26681198X-RAY DIFFRACTION100
3.3884-3.650.3241340.22631206X-RAY DIFFRACTION100
3.65-4.01710.22991350.17331217X-RAY DIFFRACTION100
4.0171-4.5980.22551370.16491231X-RAY DIFFRACTION100
4.598-5.79150.23691390.17571248X-RAY DIFFRACTION100
5.7915-48.53580.2751500.21611347X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.70290.4952-0.40873.64193.64363.9323-0.4024-0.7338-0.42521.0820.37060.0999-0.2799-0.1047-0.01950.83730.0933-0.15070.4440.05030.691481.614210.544452.1251
25.68310.54221.90736.297-4.44734.07530.1629-0.1216-0.7711-0.33120.0579-0.35670.98990.4266-0.34060.89120.1566-0.00020.4641-0.07470.706381.97167.735939.9746
36.6891-1.6692.24763.25370.21812.0651-0.28982.0460.2392-0.29420.2740.002-0.4876-0.2103-0.0560.8858-0.1459-0.02671.00310.03550.619776.080513.265613.2848
40.8621.27340.57532.21271.83213.4907-0.24331.9680.0201-0.54080.279-0.3038-0.63140.9341-0.21261.23720.16060.15651.6590.05920.483584.41019.14453.3876
59.10682.6303-2.21145.2153-2.34251.61160.27070.60440.3685-0.2451-0.3801-0.54391.729-0.43860.53240.91870.0994-0.2060.8147-0.02850.578283.68529.460816.8973
64.3672-1.1079-1.87752.96531.21891.0065-0.01221.02620.91240.4414-0.0936-0.4709-2.51870.72280.37841.1478-0.35560.04070.72480.1240.646377.85624.923721.9548
75.00160.5410.84542.09371.17830.7219-0.40940.76480.6226-0.15460.4355-0.4914-1.21230.122-0.04951.2014-0.1474-0.33630.49910.18590.967170.749626.496522.3493
84.0135-1.58260.94374.6721-4.76874.99280.0399-0.16671.0647-0.30030.39110.2942-2.6460.4205-0.63881.4458-0.1078-0.25140.76060.1030.788975.747726.786835.5879
94.00580.5581.47882.33311.18112.6063-0.53990.5571.7955-0.0531-0.14250.0042-1.23760.4754-0.64011.9407-0.9077-0.39880.58190.22461.158780.172232.238325.6433
106.8691.4324-0.40737.271-2.47148.90810.1368-0.9409-0.7586-0.15070.1033-0.79460.98241.2965-0.44231.0736-0.1409-0.23550.8593-0.01870.799489.128219.165550.5879
115.432-1.45861.97673.5102-1.70982.4985-0.2797-0.6982-0.59031.10181.3152-0.7148-0.09591.4496-0.12141.19970.2679-0.39781.9235-0.22490.437489.828822.502262.9306
124.3152-4.07120.22559.34-6.20276.5507-1.1069-0.98540.8553-1.10291.42410.3529-0.6577-0.4363-0.23910.9538-0.2816-0.11930.7607-0.10270.616182.766525.387751.7747
135.6459-1.33653.41969.4135-6.1545.8296-0.6711-0.9796-0.06331.3746-0.5527-2.2024-1.39671.83950.96331.3519-0.2588-0.45321.4152-0.03991.20697.563525.360763.0501
145.2981-2.8807-2.23867.4376-3.45617.9824-2.2488-0.3062.1927-0.38670.2471-1.2724-1.17591.43651.42651.128-0.4126-0.20571.1784-0.09971.079494.538825.689253.1561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 205 through 231 )
2X-RAY DIFFRACTION2chain 'A' and (resid 232 through 269 )
3X-RAY DIFFRACTION3chain 'A' and (resid 270 through 300 )
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 313 )
5X-RAY DIFFRACTION5chain 'A' and (resid 314 through 327 )
6X-RAY DIFFRACTION6chain 'B' and (resid 205 through 216 )
7X-RAY DIFFRACTION7chain 'B' and (resid 217 through 231 )
8X-RAY DIFFRACTION8chain 'B' and (resid 232 through 241 )
9X-RAY DIFFRACTION9chain 'B' and (resid 242 through 260 )
10X-RAY DIFFRACTION10chain 'B' and (resid 261 through 275 )
11X-RAY DIFFRACTION11chain 'B' and (resid 276 through 285 )
12X-RAY DIFFRACTION12chain 'B' and (resid 286 through 294 )
13X-RAY DIFFRACTION13chain 'B' and (resid 295 through 313 )
14X-RAY DIFFRACTION14chain 'B' and (resid 314 through 329 )

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