[English] 日本語
Yorodumi
- PDB-6yo6: Structure of iC3b1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yo6
TitleStructure of iC3b1
Components
  • hC3Nb1
  • iC3b1 alpha chain
  • iC3b1 beta chain
KeywordsIMMUNE SYSTEM / Innate Immunity / Complement system / inhibitor / nanobody / antibody
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 speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å
AuthorsJensen, R.K. / Andersen, G.R.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Danish Council for Independent Research4181-00137 Denmark
LundbeckfondenR155-2015-2666 Denmark
CitationJournal: J Immunol. / Year: 2021
Title: Complement Receptor 3 Forms a Compact High-Affinity Complex with iC3b.
Authors: Jensen, R.K. / Bajic, G. / Sen, M. / Springer, T.A. / Vorup-Jensen, T. / Andersen, G.R.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 5, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: 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
A: iC3b1 alpha chain
B: iC3b1 beta chain
C: hC3Nb1


Theoretical massNumber of molelcules
Total (without water)189,8703
Polymers189,8703
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-58 kcal/mol
Surface area71720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.450, 100.600, 136.280
Angle α, β, γ (deg.)94.230, 108.120, 113.810
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein iC3b1 alpha chain


Mass: 71407.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024*PLUS
#2: Protein iC3b1 beta chain


Mass: 104117.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024*PLUS
#3: Antibody hC3Nb1


Mass: 14345.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.61 Å3/Da / Density % sol: 78.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: 96 mM Bis-TRIS Propane pH 8.5, 4 mM Bis-TRIS Propane pH 7, 6.5 % (w/v) PEG 20.000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 6→47.592 Å / Num. obs: 9685 / % possible obs: 98.2 % / Redundancy: 3.135 % / Biso Wilson estimate: 235.6 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.182 / Χ2: 1.002 / Net I/σ(I): 5.24 / Num. measured all: 30364
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
6-6.163.1110.990.9522687367290.5621.1999
6.16-6.323.0890.8411.1321757247040.6971.01197.2
6.32-6.513.1270.7251.2720866686670.7870.86999.9
6.51-6.713.1580.6151.5621546926820.7880.73798.6
6.71-6.933.1590.4921.9319526226180.8440.58899.4
6.93-7.173.2560.4412.2421006516450.890.52699.1
7.17-7.443.2180.3772.7218605935780.8740.45397.5
7.44-7.753.2240.2963.4618965885880.920.354100
7.75-8.093.1690.2294.3617845745630.9550.27498.1
8.09-8.493.1490.1635.8116505325240.9740.19498.5
8.49-8.943.0890.1476.3615235014930.980.17698.4
8.94-9.493.1370.1237.8914624784660.9820.14897.5
9.49-10.143.0270.1069.2713414534430.9840.12897.8
10.14-10.952.9360.0989.7511984334080.9860.11894.2
10.95-122.9090.08610.5810593713640.9870.10498.1
12-13.423.0740.07612.2510853633530.9920.0997.2
13.42-15.493.3110.07312.6710103083050.9930.08799
15.49-18.973.2760.06514.428422612570.9940.07698.5
18.97-26.833.160.05215.856512092060.9950.06198.6
26.83-47.5922.9130.03718.9268110920.9960.04483.6

-
Processing

Software
NameVersionClassification
PHENIXdev_2614refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EHG

6ehg


Resolution: 6→47.592 Å / SU ML: 0.97 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 34.88
RfactorNum. reflection% reflection
Rfree0.2662 970 10.04 %
Rwork0.2408 --
obs0.2434 9657 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 473.4 Å2 / Biso mean: 315.8001 Å2 / Biso min: 240.11 Å2
Refinement stepCycle: final / Resolution: 6→47.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13131 0 0 0 13131
Num. residues----1665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03513403
X-RAY DIFFRACTIONf_angle_d1.11718173
X-RAY DIFFRACTIONf_chiral_restr0.0452050
X-RAY DIFFRACTIONf_plane_restr0.0092346
X-RAY DIFFRACTIONf_dihedral_angle_d16.4955040
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
6-6.31570.40361400.3569125698
6.3157-6.71030.32931350.3418123998
6.7103-7.22680.37131350.293125099
7.2268-7.9510.27771460.2755124899
7.951-9.09460.241380.2209122499
9.0946-11.4320.23211360.1906123897
11.432-47.5920.23011400.2125123298
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)
11.9509-2.40950.392-3.0225-0.2779-0.14850.0146-0.3352-1.02330.4584-0.454-0.88560.0836-0.421603.73770.42120.45452.65430.01463.08439.861-33.9532-16.5491
20.72571.1623-0.98110.0675-1.50190.1681-1.11130.9431.54750.49241.12860.70232.20362.692202.94540.5947-0.12913.83260.08833.157317.7071-41.7567-49.3169
31.63510.49210.58421.0188-0.19060.1293-0.21191.6191-1.6228-2.24370.7037-0.5264-2.09750.9912-03.30390.2384-0.15052.76970.14672.542521.3245-14.75775.7308
4-0.5329-0.91870.35173.98570.56283.26970.12160.0602-0.6607-0.63960.2069-0.201-1.5671-0.2579-03.62460.5166-0.06963.62850.16952.614228.1412-9.8743-1.5387
50.8973-0.46380.19633.66681.73481.7491-0.1579-0.0284-0.9658-0.5747-0.4492-0.37540.78480.4887-02.8722-0.2662-0.17583.39150.3793.090535.52226.5849-14.211
62.8992-0.89030.71441.4293-2.86560.66010.4437-0.13280.3171-0.6122-0.7793-0.33250.99571.6259-03.10140.30830.08383.56320.28392.469655.2226-8.89723.8926
70.5781-0.1103-0.51230.1095-0.8338-0.147-0.56650.36360.44390.0036-1.2778-1.9402-1.79732.5165-02.879-0.60740.02534.55580.64013.670349.1282-7.3891.9647
82.5229-0.55821.18953.7521-0.61014.16360.0434-0.16330.52160.2714-0.2322-0.1821-1.6376-0.776102.3973-0.07830.02932.36110.11552.545149.8744-72.941-65.6964
9-0.00970.48610.89595.7337-0.49653.5345-0.3489-0.8065-0.9675-0.8147-0.28020.77810.59480.391303.60460.00810.20392.2282-0.33293.334816.0911-62.8554-52.5062
101.31440.96292.8664-0.72712.1126-1.5172-0.0705-0.51510.8099-0.15180.45540.57670.52540.067603.23630.3830.65443.16390.40463.336929.8399-39.5418-27.197
114.27992.28961.46218.8252-1.33621.47620.054-0.40.0001-0.66250.44940.33630.08230.536-02.4915-0.05110.04412.80360.37512.599122.0849-6.6162-36.299
12-0.752-0.68312.05792.5491-2.74660.08480.80981.92870.9214-0.0458-2.2503-0.57530.7991-1.5253-03.0271-0.4094-0.14553.5331-0.0613.47245.8836-25.8739-60.6886
13-2.52881.5220.27310.2943.2309-1.747-0.6336-1.07660.3139-0.0891.2008-0.15870.61260.395303.3898-0.0767-0.32693.9197-0.33263.634-0.1828-47.6551-57.7814
14-0.6711-3.44461.153310.33852.20795.20041.89280.7055-1.29250.2487-1.1262-1.02581.8545-0.15130.20583.38050.46670.03984.8673-0.40594.763154.1608-41.2307-23.8874
152.40585.4432-2.72723.8941-0.93160.8091-0.48930.8193-0.7775-0.8123-0.5115-0.56140.93791.0652-03.06340.41950.30482.63290.24252.9016-1.0383-14.342916.4407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1resid 557:599 or resid 768:828 and (chain A or chain B)A0
2X-RAY DIFFRACTION2resid 600:667 and (chain A or chain B)A0
3X-RAY DIFFRACTION3resid 749:767 and (chain A or chain B)A0
4X-RAY DIFFRACTION4resid 829:933 and (chain A or chain B)A0
5X-RAY DIFFRACTION5resid 1355:1496 and (chain A or chain B)A0
6X-RAY DIFFRACTION6resid 1518:1663 and (chain A or chain B)A0
7X-RAY DIFFRACTION7resid 1497:1517 and (chain A or chain B)A0
8X-RAY DIFFRACTION8resid 989:1287 and (chain A or chain B)A0
9X-RAY DIFFRACTION9resid 23:127 and (chain A or chain B)A0
10X-RAY DIFFRACTION10resid 128:228 and (chain A or chain B)A0
11X-RAY DIFFRACTION11resid 229:351 and (chain A or chain B)A0
12X-RAY DIFFRACTION12resid 352:452 and (chain A or chain B)A0
13X-RAY DIFFRACTION13resid 453:556 and (chain A or chain B)A0
14X-RAY DIFFRACTION14(resid 934:988 or resid 1288:1354) and (chain A or chain B)A934 - 988
15X-RAY DIFFRACTION14(resid 934:988 or resid 1288:1354) and (chain A or chain B)A1288 - 1354
16X-RAY DIFFRACTION15chain CC1 - 124

+
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