[English] 日本語
Yorodumi
- PDB-7ue9: Structure of anti-C3d Fab(3d8b) in complex with C3d -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ue9
TitleStructure of anti-C3d Fab(3d8b) in complex with C3d
Components
  • Complement C3dg fragment
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / Fab / C3d
Function / homology
Function and homology information


oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / 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 / 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 / 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 / extracellular space / extracellular exosome / extracellular region / 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 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 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 / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOlland, A.M. / White, A. / Suto, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Front Immunol / Year: 2022
Title: Development and Optimization of Bifunctional Fusion Proteins to Locally Modulate Complement Activation in Diseased Tissue.
Authors: Fahnoe, K.C. / Liu, F. / Morgan, J.G. / Ryan, S.T. / Storek, M. / Stark, E.G. / Taylor, F.R. / Holers, V.M. / Thurman, J.M. / Wawersik, S. / Kalled, S.L. / Violette, S.M.
History
DepositionMar 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
C: Complement C3dg fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,91713
Polymers110,9973
Non-polymers92110
Water9,008500
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.372, 62.229, 85.547
Angle α, β, γ (deg.)90.000, 108.030, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Fab light chain


Mass: 26545.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: humanized / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab heavy chain


Mass: 49720.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Variant: humanized / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Complement C3dg fragment


Mass: 34729.656 Da / Num. of mol.: 1
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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 15% PEG 10,000, 0.1 M bicine pH 7.6

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0. 979257
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
101
29792571
ReflectionResolution: 1.75→49.47 Å / Num. obs: 73836 / % possible obs: 99.5 % / Redundancy: 3.71 % / CC1/2: 0.998 / Net I/σ(I): 15.23
Reflection shellResolution: 1.75→1.86 Å / Num. unique obs: 11680 / CC1/2: 0.699

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONT

4ont


Resolution: 1.75→49.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.212 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 3673 5 %RANDOM
Rwork0.171 ---
obs0.1725 70146 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.18 Å2 / Biso mean: 21.725 Å2 / Biso min: 12.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å2-0 Å2-0.22 Å2
2---0.12 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.75→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5741 0 60 500 6301
Biso mean--42.07 29.31 -
Num. residues----744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136021
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155640
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.6438188
X-RAY DIFFRACTIONr_angle_other_deg1.491.57713056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7715771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15823.285274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.351151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6991525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021350
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.349 238 -
Rwork0.392 4984 -
obs--96.01 %
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)
10.63930.0219-0.43320.2724-0.11371.2381-0.00370.01230.0126-0.0077-0.01090.05960.03150.00960.01450.0106-0.00160.01720.0033-0.0030.0515-17.24415.65531.378
20.92740.27120.33850.4809-0.08570.47560.011-0.0014-0.0776-0.0143-0.055-0.03490.00010.04450.0440.01650.00260.01970.01130.00920.0589-7.8113.69935.239
30.1130.0208-0.11150.1720.06340.673-0.0004-0.00490.0461-0.01320.0028-0.0020.04220.0275-0.00240.01580.01590.01790.0210.01750.039844.31635.141-2.063
40.93660.3217-0.65480.2153-0.03120.85650.0452-0.07210.00120.0055-0.0784-0.0201-0.044-0.00040.03320.07360.05450.01260.1090.08880.138215.6431.47524.902
50.20890.0498-0.13540.0518-0.03970.11320.00110.00410.0423-0.00360.00990.01980.02050.0064-0.0110.01810.00840.01520.02160.0050.028115.95325.69119.388
60.62650.2402-0.45120.1564-0.20671.229-0.0229-0.06390.02810.00090.034-0.00990.09480.0716-0.01110.02230.01860.01830.0618-0.01770.051119.65126.24837.496
70.99550.43340.63590.71440.15281.1847-0.05010.08640.0484-0.07520.11720.0365-0.0385-0.0328-0.06710.0159-0.01090.0120.0270.01440.039611.43932.0217.51
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L112 - 219
2X-RAY DIFFRACTION2H112 - 214
3X-RAY DIFFRACTION3C0 - 310
4X-RAY DIFFRACTION4C401 - 404
5X-RAY DIFFRACTION4H501 - 503
6X-RAY DIFFRACTION4L301 - 303
7X-RAY DIFFRACTION5C501 - 661
8X-RAY DIFFRACTION5H601 - 775
9X-RAY DIFFRACTION5L401 - 564
10X-RAY DIFFRACTION6H1 - 111
11X-RAY DIFFRACTION7L1 - 111

+
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://pdbjlvh1.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