[English] 日本語
Yorodumi
- PDB-9n1z: Structure of C3d Bound to a Fragment of FHR-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n1z
TitleStructure of C3d Bound to a Fragment of FHR-2
Components
  • Complement C3dg fragment
  • Complement factor H-related protein 2
KeywordsIMMUNE SYSTEM / complement system / C3 / RCA / inhibitor
Function / homology
Function and homology information


C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / complement component C3b binding / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of phagocytosis, engulfment ...C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / complement component C3b binding / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of phagocytosis, engulfment / Activation of C3 and C5 / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / complement receptor mediated signaling pathway / positive regulation of D-glucose transmembrane transport / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / : / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / negative regulation of protein binding / Purinergic signaling in leishmaniasis infection / Regulation of Complement cascade / Peptide ligand-binding receptors / Post-translational protein phosphorylation / response to bacterium / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / inflammatory response / receptor ligand activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / 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 / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. ...: / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C3 / Complement factor H-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsDuan, H. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: J Immunol. / Year: 2025
Title: The C-terminal domain of Staphylococcus aureus Efb recruits FHR-2 to C3b, synergistically inhibiting the terminal complement pathway.
Authors: Duan, H. / Kortvely, E. / Mary, J.L. / Hauck, S.M. / Geisbrecht, B.V.
History
DepositionJan 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement C3dg fragment
B: Complement factor H-related protein 2
C: Complement C3dg fragment
D: Complement factor H-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9978
Polymers95,6134
Non-polymers3844
Water6,539363
1
A: Complement C3dg fragment
B: Complement factor H-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0955
Polymers47,8062
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Complement C3dg fragment
D: Complement factor H-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9023
Polymers47,8062
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.302, 116.228, 165.582
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-1449-

HOH

21A-1458-

HOH

31A-1463-

HOH

41A-1513-

HOH

-
Components

#1: Protein Complement C3dg fragment


Mass: 33143.879 Da / Num. of mol.: 2 / Mutation: C1010A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01024
#2: Protein Complement factor H-related protein 2 / FHR-2 / DDESK59 / H factor-like 3 / H factor-like protein 2


Mass: 14662.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFHR2, CFHL2, FHR2, HFL3 / Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36980
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.075 M HEPES [PH 7.5] 1.2 M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 47909 / % possible obs: 99.2 % / Redundancy: 11.2 % / CC1/2: 0.946 / CC star: 0.986 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.079 / Rrim(I) all: 0.277 / Χ2: 1.039 / Net I/σ(I): 6.7 / Num. measured all: 537249
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.387.60.95146140.5980.8650.3561.0211.06496.9
2.38-2.488.30.85846090.8440.9570.3020.9131.07297.1
2.48-2.598.60.88647360.8150.9480.3130.9431.08198.4
2.59-2.7311.50.89647550.8960.9720.2790.941.01599.8
2.73-2.912.90.86348120.940.9840.2470.8981.076100
2.9-3.1213.20.51348160.9750.9940.1470.5341.047100
3.12-3.4412.80.33847940.9780.9950.0980.3521.029100
3.44-3.9311.80.19548310.990.9980.0580.2041.0399.9
3.93-4.9513.10.11848900.9950.9990.0340.1230.988100
4.95-50120.08450520.9950.9990.0250.0881.02899.8

-
Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→47.57 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 2002 4.22 %
Rwork0.1943 --
obs0.1957 47435 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6493 0 20 363 6876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036650
X-RAY DIFFRACTIONf_angle_d0.5589008
X-RAY DIFFRACTIONf_dihedral_angle_d4.592877
X-RAY DIFFRACTIONf_chiral_restr0.039983
X-RAY DIFFRACTIONf_plane_restr0.0041160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.26881240.24642952X-RAY DIFFRACTION90
2.36-2.430.30581420.24643070X-RAY DIFFRACTION95
2.43-2.50.27451380.2423115X-RAY DIFFRACTION96
2.5-2.580.2761420.24123177X-RAY DIFFRACTION97
2.58-2.670.29961350.2273231X-RAY DIFFRACTION98
2.67-2.780.27361480.22123270X-RAY DIFFRACTION99
2.78-2.910.23941510.21223287X-RAY DIFFRACTION99
2.91-3.060.23481450.20953242X-RAY DIFFRACTION100
3.06-3.250.22391410.20143312X-RAY DIFFRACTION100
3.25-3.50.21251470.18813294X-RAY DIFFRACTION100
3.5-3.850.2141470.17853321X-RAY DIFFRACTION100
3.85-4.410.1961460.15973310X-RAY DIFFRACTION100
4.41-5.550.18921490.16493365X-RAY DIFFRACTION100
5.56-47.570.22691470.19783487X-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)
13.1393-0.2609-1.97755.6086-0.11794.0864-0.04310.10341.08390.32460.23690.3384-0.96080.1386-0.2220.50060.0087-0.15930.27820.07540.5278-11.569258.240825.3137
22.6329-0.3598-0.65454.0216-0.16732.3384-0.0835-0.31230.69070.3068-0.08710.1764-0.5173-0.19610.05590.41090.0559-0.06040.2039-0.03750.3495-8.431557.457130.3891
33.64910.43340.46414.16960.47934.0643-0.0366-0.50860.45640.54270.10360.4444-0.2425-0.27770.01680.24030.01520.01760.279-0.0190.2149-13.024347.972734.7592
42.9967-0.7257-0.05852.2462-0.12932.73830.0399-0.1374-0.03520.02080.0328-0.02030.27010.01290.01780.27040.0166-0.02060.20080.01650.1811-1.628537.404628.1289
53.5571-0.95580.26311.9456-0.02811.94020.00930.74780.0458-0.3155-0.0504-0.11240.23130.22670.03360.35380.0143-0.01620.39120.02620.22532.097738.707513.7354
63.4631-0.6173-0.23763.1178-1.25344.5867-0.0896-0.08080.20570.2173-0.0515-0.3480.09940.44620.04820.2742-0.0216-0.0220.27730.00980.28019.164841.644726.593
73.3221-0.49250.09773.5135-1.5355.0559-0.15660.34860.2044-0.2489-0.2132-0.72960.07760.87660.13150.23510.03950.02090.55320.00390.348517.582442.37818.2491
81.9815-0.3019-0.47252.568-0.21742.6639-0.09360.73540.7036-0.25950.0486-0.4626-0.35820.54740.07520.3501-0.0939-0.00010.42120.12290.415910.076755.464714.0053
92.67710.46550.00412.70520.26932.1869-0.05440.31830.9991-0.17520.0718-0.2328-0.85510.27280.02130.5337-0.079-0.05540.29750.10770.5971.343463.890617.4832
102.51720.7468-0.36673.57280.78414.4128-0.0192-0.09720.79320.24210.0518-0.315-0.63410.4601-0.01210.3188-0.0454-0.10920.2459-0.02970.44181.363859.116624.9411
118.18791.2984-4.72796.0582-0.95932.73850.354-0.3658-0.35120.5789-0.3811-0.19230.56040.92520.0640.52830.1319-0.10320.2319-0.08420.274816.179225.512942.5084
121.95840.3153-1.78031.33171.26367.37730.26560.221-0.26730.148-0.1095-0.12230.85210.1667-0.08920.54060.1334-0.07110.3128-0.05050.2713.760522.557334.5039
138.9568-3.3144-5.36845.17732.54025.88870.2799-0.29950.6220.72860.23340.0196-1.0131-1.1242-0.33440.81730.33360.02940.7319-0.03290.398522.139728.25511.7692
143.9525-1.2152-4.70171.44511.54015.6101-0.09620.3077-0.04980.37490.09610.1006-0.0409-0.8250.25660.55710.2153-0.01220.7402-0.05530.275519.010421.11298.1544
155.5425-2.0731-4.32343.3271.66847.9857-0.1828-0.30880.35780.1799-0.0148-0.1771-0.3289-0.4907-0.13510.33630.0455-0.04480.2999-0.11810.283429.328520.2889-0.2967
167.8975.2412-6.03697.2616-4.86534.8059-0.3677-0.49150.24820.1-0.03580.04680.3139-0.01720.37910.4350.2514-0.07570.5844-0.15130.318628.644122.5687.4922
172.4522-0.04130.29630.8606-0.24370.1014-0.2466-0.10050.3236-0.0820.10660.6833-0.308-0.83-0.30290.86960.644-0.51531.5018-0.40371.1212-2.86858.590513.6441
182.05270.13120.22942.68520.65530.8017-0.285-0.90770.4450.0112-0.24840.6399-0.5884-1.08620.03960.46350.2439-0.12320.7964-0.18110.458413.6479-1.229121.0987
193.2559-0.8908-2.15812.77750.80761.4578-0.0895-0.7334-0.63950.1618-0.04460.45770.2384-1.14290.20240.3475-0.1333-0.02611.08750.0410.50599.0201-14.615920.2751
200.9892-1.2514-0.04591.57780.05710.00050.0114-0.4496-0.50.33060.0061.10730.1124-0.94170.52240.5297-0.13350.12041.9088-0.20131.1398-4.5324-17.468525.2578
212.8116-1.8593-0.22571.6106-0.37050.72250.12040.0002-0.5923-0.06770.29090.34320.0158-0.15340.21120.48170.1638-0.07681.9948-0.4041.0046-9.9537-7.783220.462
227.94111.1031-2.26997.0998-5.29537.0959-0.33080.6531-0.0717-0.59630.2691-0.23460.7656-0.01480.05180.3304-0.0468-0.01580.2961-0.08890.227829.3789-12.63910.5771
233.591.2103-2.47292.8779-2.17927.99930.0190.0531-0.1657-0.0363-0.0766-0.0474-0.02050.0124-0.00450.167-0.0166-0.05280.2102-0.00230.185931.5233-11.29519.0897
241.671-2.28221.4846.4549-5.70595.3751-0.0481-0.35560.02310.16090.35290.73770.0232-0.8376-0.37450.4382-0.1423-0.00780.69150.0520.286626.9728-23.64537.0064
254.8867-1.3788-2.50157.4902-3.46356.39890.2235-0.4523-0.0634-0.04260.02570.33720.5591-0.0676-0.14910.4308-0.2093-0.09860.42340.09750.228432.9193-30.016641.1172
266.0789-0.1775-2.29089.6694-5.46484.57250.01640.1848-0.1358-0.71130.17960.21281.2994-0.4499-0.25220.5716-0.2806-0.11850.53960.02450.317530.5877-30.329733.9612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 992 through 1012 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1013 through 1038 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1039 through 1059 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1060 through 1110 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1111 through 1138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1139 through 1164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1165 through 1182 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1183 through 1243 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1244 through 1268 )
10X-RAY DIFFRACTION10chain 'A' and (resid 1269 through 1287 )
11X-RAY DIFFRACTION11chain 'B' and (resid 146 through 157 )
12X-RAY DIFFRACTION12chain 'B' and (resid 158 through 210 )
13X-RAY DIFFRACTION13chain 'B' and (resid 211 through 228 )
14X-RAY DIFFRACTION14chain 'B' and (resid 229 through 241 )
15X-RAY DIFFRACTION15chain 'B' and (resid 242 through 256 )
16X-RAY DIFFRACTION16chain 'B' and (resid 257 through 269 )
17X-RAY DIFFRACTION17chain 'C' and (resid 994 through 1059 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1060 through 1138 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1139 through 1198 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1199 through 1242 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1243 through 1285 )
22X-RAY DIFFRACTION22chain 'D' and (resid 146 through 157 )
23X-RAY DIFFRACTION23chain 'D' and (resid 158 through 210 )
24X-RAY DIFFRACTION24chain 'D' and (resid 211 through 235 )
25X-RAY DIFFRACTION25chain 'D' and (resid 236 through 256 )
26X-RAY DIFFRACTION26chain 'D' and (resid 257 through 269 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more