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- PDB-2v8e: Crystal structure of Human Complement Factor H, SCR domains 6-8 (... -

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Basic information

Entry
Database: PDB / ID: 2v8e
TitleCrystal structure of Human Complement Factor H, SCR domains 6-8 (H402 risk variant), in complex with ligand.
ComponentsCOMPLEMENT FACTOR HFactor H
KeywordsIMMUNE SYSTEM / ALTERNATIVE SPLICING / SUCROSE OCTASULPHATE / AGE-RELATED MACULAR DEGENERATION / SUSHI / SECRETED / FACTOR H / COMPLEMENT / POLYMORPHISM / COMPLEMENT ALTERNATE PATHWAY / DISEASE MUTATION / GLYCOSAMINOGLYCAN / GLYCOPROTEIN / INNATE IMMUNITY / IMMUNE RESPONSE
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/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
sucrose octasulfate / Complement factor H
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsProsser, B.E. / Johnson, S. / Roversi, P. / Herbert, A.P. / Blaum, B.S. / Tyrrell, J. / Jowitt, T.A. / Clark, S.J. / Tarelli, E. / Uhrin, D. ...Prosser, B.E. / Johnson, S. / Roversi, P. / Herbert, A.P. / Blaum, B.S. / Tyrrell, J. / Jowitt, T.A. / Clark, S.J. / Tarelli, E. / Uhrin, D. / Barlow, P.N. / Sim, R.B. / Day, A.J. / Lea, S.M.
CitationJournal: J.Exp.Med. / Year: 2007
Title: Structural Basis for Complement Factor H Linked Age-Related Macular Degeneration.
Authors: Prosser, B.E. / Johnson, S. / Roversi, P. / Herbert, A.P. / Blaum, B.S. / Tyrrell, J. / Jowitt, T.A. / Clark, S.J. / Tarelli, E. / Uhrin, D. / Barlow, P.N. / Sim, R.B. / Day, A.J. / Lea, S.M.
History
DepositionAug 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / software / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _software.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMPLEMENT FACTOR H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7228
Polymers21,2881
Non-polymers1,4347
Water82946
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.000, 92.500, 57.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein COMPLEMENT FACTOR H / Factor H / H FACTOR 1 / HUMAN COMPLEMENT FACTOR H


Mass: 21287.537 Da / Num. of mol.: 1 / Fragment: DOMAINS 6,7 AND 8, RESIDUES 322-506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-14B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P08603
#2: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 52 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS IS RESIDUES 321-505 OF THE ABOVE ENTRY WITH AN N- TERMINAL METHIONINE. RESIDUES 400, 402 AND ...THIS IS RESIDUES 321-505 OF THE ABOVE ENTRY WITH AN N- TERMINAL METHIONINE. RESIDUES 400, 402 AND 493 ARE POLYMORPHIC.

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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: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 4.5 / Details: 0.1M SODIUM ACETATE, PH4.5, 20% (W/V) PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→35.9 Å / Num. obs: 7083 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 6.136 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameClassification
DMmodel building
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
SHARP-SOLOMONphasing
BUSTER-TNTphasing
DMphasing
piratephasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JGW

2jgw


Resolution: 2.5→15 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: BUSTER-TNT-GELLY 2.1.1 E. BLANC, P. ROVERSI, C. VONRHEIN, C. FLENSBURG, S. M. LEA AND G.BRICOGNE
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 691 9.8 %0.2255
Rwork0.2233 ---
all0.2255 ---
obs0.2233 7044 --
Solvent computationSolvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.43 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 78 46 1603
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01516081
X-RAY DIFFRACTIONt_angle_deg1.35521902
X-RAY DIFFRACTIONt_dihedral_angle_d18.6772850
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.003322
X-RAY DIFFRACTIONt_gen_planes0.0152475
X-RAY DIFFRACTIONt_it1.972160820
X-RAY DIFFRACTIONt_nbd0.168385
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact

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