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- PDB-2xqw: Structure of Factor H domains 19-20 in complex with complement C3d -

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Basic information

Entry
Database: PDB / ID: 2xqw
TitleStructure of Factor H domains 19-20 in complex with complement C3d
Components
  • COMPLEMENT C3
  • COMPLEMENT FACTOR H
KeywordsIMMUNE SYSTEM / COMPLEMENT ALTERNATIVE PATHWAY / ATYPICAL HEMOLYTIC UREMIC SYNDROME / AHUS / CFH / FH / C3B
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / symbiont cell surface / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance ...regulation of complement activation, alternative pathway / symbiont cell surface / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / regulation of complement activation / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / heparin binding / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement Module, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 ...: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement Module, domain 1 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Complement Module; domain 1 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Ribbon / Immunoglobulin-like fold / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Complement C3 / Complement factor H
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsKajander, T. / Lehtinen, M.J. / Hyvarinen, S. / Bhattacharjee, A. / Leung, E. / Isenman, D.E. / Meri, S. / Jokiranta, T.S. / Goldman, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Dual Interaction of Factor H with C3D and Glycosaminoglycans in Host-Nonhost Discrimination by Complement.
Authors: Kajander, T. / Lehtinen, M.J. / Hyvarinen, S. / Bhattacharjee, A. / Leung, E. / Isenman, D.E. / Meri, S. / Goldman, A. / Jokiranta, T.S.
#1: Journal: 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. / Lehtinen, M.J. / Parepalo, M. / Meri, S. / Goldman, A.
#2: Journal: J.Biol.Chem. / Year: 2009
Title: Mutations of Factor H Impair Regulation of Surface- Bound C3B by Three Mechanisms in Atypical Hemolytic Uremic Syndrome.
Authors: Lehtinen, M.J. / Rops, A.L. / Isenman, D.E. / Van Der Vlag, J. / Jokiranta, T.S.
History
DepositionSep 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMPLEMENT C3
B: COMPLEMENT C3
C: COMPLEMENT FACTOR H


Theoretical massNumber of molelcules
Total (without water)80,7823
Polymers80,7823
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint0.6 kcal/mol
Surface area35440 Å2
MethodPISA
2
A: COMPLEMENT C3


Theoretical massNumber of molelcules
Total (without water)32,8991
Polymers32,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: COMPLEMENT C3


Theoretical massNumber of molelcules
Total (without water)32,8991
Polymers32,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: COMPLEMENT FACTOR H


Theoretical massNumber of molelcules
Total (without water)14,9841
Polymers14,9841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.554, 103.554, 141.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.83692, 0.41801, 0.35331), (-0.18051, 0.82021, -0.54283), (-0.5167, 0.39054, 0.76191)
Vector: 41.98795, 19.24354, -16.83389)

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Components

#1: Protein COMPLEMENT C3 / C3 AND PZP-LIKE ALPHA-2-MACROGLOBULIN DOMAIN-CONTAINING PROTEIN 1


Mass: 32898.734 Da / Num. of mol.: 2 / Fragment: THIOESTER DOMAIN, RESIDUES 996-1287 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01024
#2: Protein COMPLEMENT FACTOR H / H FACTOR 1


Mass: 14984.093 Da / Num. of mol.: 1 / Fragment: DOMAINS 19-20, RESIDUES 1103-1231 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P08603
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS1010 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS1010 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS1010 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS1010 TO ALA ENGINEERED RESIDUE IN CHAIN C, ASP1119 TO GLY ENGINEERED RESIDUE IN CHAIN C, GLN1139 TO ALA
Sequence detailsCHAIN A AND B HAVE A POINT MUTATION C17A AND FRAGMENT CRYSTALLIZED HAS RESIDUES N-TERMINAL FROM CD3 ...CHAIN A AND B HAVE A POINT MUTATION C17A AND FRAGMENT CRYSTALLIZED HAS RESIDUES N-TERMINAL FROM CD3 GIVEN IN UNP P01024 (RESIDUES 1002-1303). CHAIN C FIRST FOUR RESIDUES COME FROM THE EXPRESSION VECTOR, AND HAS MUTATIONS D1119G, Q1139A.

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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: 2.71 Å3/Da / Density % sol: 54.54 % / Description: NONE
Crystal growTemperature: 295 K / pH: 7.5
Details: 12-18% PEG 4000, 0.1 M HEPES, PH 7.5, AT 22 DEGREES C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.983
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 37791 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 43.65 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.36 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3D

1c3d


Resolution: 2.306→41.753 Å / SU ML: 0.38 / σ(F): 1.39 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 3723 5 %
Rwork0.2005 --
obs0.2026 36767 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.214 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 53.18 Å2
Baniso -1Baniso -2Baniso -3
1-5.7952 Å20 Å20 Å2
2--5.7952 Å20 Å2
3----11.5904 Å2
Refinement stepCycle: LAST / Resolution: 2.306→41.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5507 0 0 193 5700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065634
X-RAY DIFFRACTIONf_angle_d0.967643
X-RAY DIFFRACTIONf_dihedral_angle_d18.572008
X-RAY DIFFRACTIONf_chiral_restr0.067852
X-RAY DIFFRACTIONf_plane_restr0.005985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3055-2.33470.33981240.30892347X-RAY DIFFRACTION90
2.3347-2.36540.35581380.29412594X-RAY DIFFRACTION100
2.3654-2.39780.29831370.28792634X-RAY DIFFRACTION100
2.3978-2.43210.33721360.27592603X-RAY DIFFRACTION100
2.4321-2.46840.33391390.26462657X-RAY DIFFRACTION100
2.4684-2.50690.29481370.25142596X-RAY DIFFRACTION100
2.5069-2.5480.29031370.24842591X-RAY DIFFRACTION100
2.548-2.59190.25621400.23822674X-RAY DIFFRACTION100
2.5919-2.63910.27731360.23992586X-RAY DIFFRACTION100
2.6391-2.68980.28781400.25612630X-RAY DIFFRACTION100
2.6898-2.74470.32251380.24082582X-RAY DIFFRACTION100
2.7447-2.80440.25781400.23842655X-RAY DIFFRACTION100
2.8044-2.86960.31921380.22822618X-RAY DIFFRACTION100
2.8696-2.94140.26381400.22492612X-RAY DIFFRACTION100
2.9414-3.02090.20771390.21132658X-RAY DIFFRACTION100
3.0209-3.10970.27691370.21512592X-RAY DIFFRACTION100
3.1097-3.21010.26641410.21452662X-RAY DIFFRACTION100
3.2101-3.32470.29221360.20782596X-RAY DIFFRACTION100
3.3247-3.45780.22191400.21812644X-RAY DIFFRACTION100
3.4578-3.61510.24031390.19132609X-RAY DIFFRACTION100
3.6151-3.80560.19551400.19012687X-RAY DIFFRACTION100
3.8056-4.04380.25671340.1772549X-RAY DIFFRACTION100
4.0438-4.35570.20171410.17242646X-RAY DIFFRACTION100
4.3557-4.79350.21221360.1572624X-RAY DIFFRACTION100
4.7935-5.48580.22741410.16322642X-RAY DIFFRACTION100
5.4858-6.90650.20541410.17732624X-RAY DIFFRACTION100
6.9065-41.76020.17391380.15252575X-RAY DIFFRACTION98

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