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- PDB-3rj3: Complement components factor H CCP19-20 (S1191L mutant) and C3D i... -

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Basic information

Entry
Database: PDB / ID: 3rj3
TitleComplement components factor H CCP19-20 (S1191L mutant) and C3D in complex
Components
  • Complement C3d fragment
  • Complement Factor H-related protein 1
KeywordsPROTEIN BINDING / C3d-ALPHA-ALPHA BARREL / COMPLEMENT COMPONENT / FACTOR H
Function / homology
Function and homology information


regulation of complement activation, alternative pathway / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / symbiont cell surface / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation ...regulation of complement activation, alternative pathway / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / symbiont cell surface / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / regulation of complement-dependent cytotoxicity / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / regulation of complement activation / complement component C3b binding / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement receptor mediated signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / heparan sulfate proteoglycan binding / serine-type endopeptidase complex / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / neuron remodeling / cytolysis by host of symbiont cells / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / negative regulation of protein binding / Peptide ligand-binding receptors / Regulation of Complement cascade / response to bacterium / Post-translational protein phosphorylation / fatty acid metabolic process / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein phosphorylation / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / heparin binding / secretory granule lumen / G alpha (i) signalling events / blood microparticle / immune response / G protein-coupled receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / inflammatory response / 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 C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 ...: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Complement Module, domain 1 / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / 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 / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Glycosyltransferase - #20 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / Complement factor H-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMorgan, H.P. / Hannan, J.P.
CitationJournal: Biochemistry / Year: 2012
Title: Structural and functional characterization of the product of disease-related factor h gene conversion.
Authors: Herbert, A.P. / Kavanagh, D. / Johansson, C. / Morgan, H.P. / Blaum, B.S. / Hannan, J.P. / Barlow, P.N. / Uhrin, D.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3d fragment
B: Complement C3d fragment
C: Complement C3d fragment
D: Complement Factor H-related protein 1
E: Complement Factor H-related protein 1
F: Complement Factor H-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,10110
Polymers150,7336
Non-polymers3684
Water6,702372
1
A: Complement C3d fragment
D: Complement Factor H-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3363
Polymers50,2442
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C3d fragment
F: Complement Factor H-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3363
Polymers50,2442
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C3d fragment
E: Complement Factor H-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4284
Polymers50,2442
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.750, 82.620, 85.400
Angle α, β, γ (deg.)112.61, 110.26, 99.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Complement C3d fragment / C3D


Mass: 35444.438 Da / Num. of mol.: 3 / Fragment: UNP residues 996-1303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01024
#2: Protein Complement Factor H-related protein 1 / FHR-1 / H factor-like protein 1 / H-factor-like 1 / H36


Mass: 14799.873 Da / Num. of mol.: 3 / Fragment: UNP residues 206-330
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, UniProt: P08603*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNATURAL VARIANT

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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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 4% w/v PEG 8000, 0.1 M Tris HCl, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
PH range: pH 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50.47 Å / Num. obs: 69803 / % possible obs: 94.8 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 3.9 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.087 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.2 / Num. unique all: 32973 / Rsym value: 0.699 / % possible all: 83.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.2_432) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OXU

3oxu


Resolution: 2.35→41.604 Å / SU ML: 0.39 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 3357 5.05 %RANDOM
Rwork0.1905 ---
obs0.1926 66478 96.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.335 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9921 Å21.1871 Å2-0.1729 Å2
2---0.7476 Å2-0.4811 Å2
3---2.7398 Å2
Refinement stepCycle: LAST / Resolution: 2.35→41.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9771 0 24 372 10167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110134
X-RAY DIFFRACTIONf_angle_d0.73313722
X-RAY DIFFRACTIONf_dihedral_angle_d15.8063789
X-RAY DIFFRACTIONf_chiral_restr0.0551504
X-RAY DIFFRACTIONf_plane_restr0.0021769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.38370.35531240.32422366X-RAY DIFFRACTION87
2.3837-2.41930.30861470.30452631X-RAY DIFFRACTION97
2.4193-2.45710.37071470.28612625X-RAY DIFFRACTION97
2.4571-2.49730.32851160.26512655X-RAY DIFFRACTION97
2.4973-2.54040.30621400.24532633X-RAY DIFFRACTION96
2.5404-2.58660.2761470.24232675X-RAY DIFFRACTION97
2.5866-2.63630.31351350.23512579X-RAY DIFFRACTION97
2.6363-2.69010.31791550.23892645X-RAY DIFFRACTION96
2.6901-2.74860.25461440.23382692X-RAY DIFFRACTION97
2.7486-2.81250.30131320.21832589X-RAY DIFFRACTION97
2.8125-2.88280.251510.2142642X-RAY DIFFRACTION96
2.8828-2.96080.25891380.20052652X-RAY DIFFRACTION97
2.9608-3.04790.25311320.20072661X-RAY DIFFRACTION97
3.0479-3.14620.24421540.18392627X-RAY DIFFRACTION97
3.1462-3.25860.21091210.18482662X-RAY DIFFRACTION97
3.2586-3.3890.22691380.18992655X-RAY DIFFRACTION97
3.389-3.54320.24051480.18342643X-RAY DIFFRACTION97
3.5432-3.72990.24061390.18852632X-RAY DIFFRACTION97
3.7299-3.96340.21671460.17362637X-RAY DIFFRACTION97
3.9634-4.26910.18631430.16592627X-RAY DIFFRACTION97
4.2691-4.69820.15971310.14182671X-RAY DIFFRACTION97
4.6982-5.37680.19291520.14872613X-RAY DIFFRACTION96
5.3768-6.76950.22351310.20672645X-RAY DIFFRACTION96
6.7695-41.61050.21011460.16732664X-RAY DIFFRACTION98
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)
11.27250.42520.45110.84660.66251.08670.0188-0.17450.19290.13250.1092-0.0373-0.06110.1757-0.1060.2283-0.03070.01640.222-0.04280.235237.6875-46.772336.2908
20.3347-0.427-0.16750.99070.89350.6050.0636-0.01230.06520.0761-0.038-0.0047-0.0432-0.0713-0.02340.1901-0.03550.01750.16990.01730.198430.0777-62.539134.5247
30.60730.04910.43861.14660.01480.95230.03790.0687-0.1114-0.1561-0.04860.10070.14130.03450.00150.26420.01060.00750.2248-0.02710.223432.01-66.681820.8065
41.4420.4395-0.37281.1325-0.26910.99860.1340.19120.2534-0.27880.05060.0181-0.3078-0.0012-0.14850.3567-0.00850.02870.25590.01240.221834.0503-50.076815.9534
50.9352-0.47190.12760.8462-0.30860.54790.1110.118-0.0151-0.1485-0.12440.0020.0350.03240.01220.1925-0.00950.01290.2255-0.00740.1481-0.5458-29.185933.0904
61.33570.01440.47641.6546-0.13761.975-0.0834-0.0571-0.34450.00780.2037-0.05670.3982-0.0335-0.07890.2632-0.02460.0070.16430.0450.2117-4.9148-44.617444.9028
72.62410.7220.61030.56660.96712.2908-0.0540.2019-0.6906-0.14640.15950.29120.5555-0.2046-0.15210.4941-0.0262-0.06110.3036-0.08340.4094-5.3454-50.863129.9417
81.35980.0334-0.0010.74070.90071.7570.17230.1536-0.3448-0.1887-0.085-0.03540.49170.0162-0.07730.44060.0904-0.01730.3299-0.05790.26341.8036-44.751324.3652
90.6993-0.1802-0.25550.12860.39870.79310.16360.10950.3075-0.0153-0.1238-0.2138-0.1997-0.0419-0.03560.25310.02130.01720.20950.07990.381749.25912.959620.1206
100.2968-0.5766-0.28293.28730.6920.59540.21140.2852-0.30960.0277-0.35970.5613-0.0083-0.23160.10240.24510.0062-0.06910.34410.00650.504434.7442-8.66125.7705
112.1027-0.1161-0.11670.63640.30581.15280.21520.4892-0.4941-0.1048-0.13020.08480.02470.0163-0.07670.24860.0886-0.0870.3033-0.14320.344741.8739-15.197311.9579
123.1029-2.3297-0.4072.22670.52070.30160.44260.35240.1065-0.5295-0.1485-0.1585-0.16550.125-0.14270.45050.1496-0.0370.54980.02060.39246.7598-3.71418.1
133.33740.42660.93560.1456-0.22251.62720.2206-0.7083-0.52370.0545-0.1708-0.0010.0473-0.12520.01310.1917-0.005-0.02570.3107-0.02470.287157.8175-17.769543.7949
144.87381.573-1.03521.43570.26020.5006-0.0697-0.65980.25750.1223-0.01530.1149-0.01950.12650.06870.2513-0.02160.01150.2939-0.01380.249852.2377-16.779646.9463
152.08421.00080.26881.4653-0.01080.1090.0557-0.18180.4502-0.1357-0.02520.23040.01520.019-0.04490.2837-0.00750.06440.2694-0.03160.371223.3357-32.491438.9394
161.31861.17980.46432.2323-0.10460.13050.3271-0.3541-0.10650.3817-0.2051-0.10860.0862-0.055-0.07730.3156-0.01370.05220.28520.03220.307726.8171-38.525245.2608
170.9879-0.41620.13870.45190.22570.4378-0.2062-0.0621-0.30270.21460.0445-0.0090.03380.05130.11840.3277-0.0114-0.00450.26290.03110.380125.6312-0.716540.9737
181.9141.14021.5031.20910.213.11110.1995-0.2579-0.9422-0.13670.1253-0.32560.5334-0.3684-0.23470.44410.0023-0.00940.31050.12610.485427.8273-8.102343.9528
192.5708-0.10181.26780.30670.42470.9979-0.17680.28240.0573-0.07790.0748-0.0476-0.21150.07220.08060.2933-0.0451-0.00220.28610.07390.3088-1.3249-8.505122.8506
203.4538-0.21772.27830.60740.49182.12060.38510.9438-0.2075-0.11140.13260.1359-0.11670.372-0.30110.4211-0.00550.03310.51530.06240.3544-2.4861-13.188617.9538
211.79031.60470.86721.93980.71821.07290.0726-0.2546-0.04830.42820.1814-0.3569-0.27440.2787-0.19780.4252-0.0815-0.02430.5732-0.11040.36857.5117-21.145559.9999
220.09010.03690.01170.6968-0.21070.06030.1071-0.6617-0.06880.676-0.1823-0.3351-0.51020.39050.09340.7178-0.2054-0.08280.8166-0.10020.42795.1076-24.657966.3244
231.9552-1.56170.98622.1703-1.97986.74110.7907-0.1395-0.0729-0.14540.34950.4139-0.0272-1.1781-0.49870.4749-0.05530.13440.74290.11840.6328-22.1835-33.213764.1668
242.99450.82481.1852.77082.34032.16080.228-0.5096-0.5973-0.22990.27060.1158-0.97730.3845-0.2880.6788-0.13030.0150.63740.16090.2693-16.6169-35.18271.5212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:78)
2X-RAY DIFFRACTION2(chain A and resid 79:141)
3X-RAY DIFFRACTION3(chain A and resid 142:216)
4X-RAY DIFFRACTION4(chain A and resid 217:294)
5X-RAY DIFFRACTION5(chain B and resid 10:141)
6X-RAY DIFFRACTION6(chain B and resid 142:227)
7X-RAY DIFFRACTION7(chain B and resid 228:270)
8X-RAY DIFFRACTION8(chain B and resid 271:309)
9X-RAY DIFFRACTION9(chain C and resid 1:116)
10X-RAY DIFFRACTION10(chain C and resid 117:143)
11X-RAY DIFFRACTION11(chain C and resid 144:270)
12X-RAY DIFFRACTION12(chain C and resid 271:294)
13X-RAY DIFFRACTION13(chain D and resid 1107:1119)
14X-RAY DIFFRACTION14(chain D and resid 1120:1168)
15X-RAY DIFFRACTION15(chain D and resid 1169:1206)
16X-RAY DIFFRACTION16(chain D and resid 1207:1231)
17X-RAY DIFFRACTION17(chain E and resid 1107:1146)
18X-RAY DIFFRACTION18(chain E and resid 1147:1163)
19X-RAY DIFFRACTION19(chain E and resid 1164:1221)
20X-RAY DIFFRACTION20(chain E and resid 1222:1231)
21X-RAY DIFFRACTION21(chain F and resid 1107:1153)
22X-RAY DIFFRACTION22(chain F and resid 1154:1167)
23X-RAY DIFFRACTION23(chain F and resid 1168:1218)
24X-RAY DIFFRACTION24(chain F and resid 1219:1228)

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