[English] 日本語
Yorodumi
- PDB-2iwg: COMPLEX BETWEEN THE PRYSPRY DOMAIN OF TRIM21 AND IGG FC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iwg
TitleCOMPLEX BETWEEN THE PRYSPRY DOMAIN OF TRIM21 AND IGG FC
Components
  • 52 KDA RO PROTEIN
  • IG GAMMA-1 CHAIN C
KeywordsIMMUNOGLOBULIN DOMAIN / ZINC / RNA-BINDING / ZINC-FINGER / DNA-BINDING / RIBONUCLEOPROTEIN / IMMUNOGLOBULIN C REGION / SYSTEMIC LUPUS ERYTHEMATOSUS / POLYMORPHISM / GLYCOPROTEIN / METAL-BINDING
Function / homology
Function and homology information


suppression of viral release by host / protein K27-linked ubiquitination / negative regulation of protein deubiquitination / regulation of type I interferon production / negative regulation of viral transcription / protein K6-linked ubiquitination / Fc-gamma receptor I complex binding / cellular response to chemical stress / STING mediated induction of host immune responses / complement-dependent cytotoxicity ...suppression of viral release by host / protein K27-linked ubiquitination / negative regulation of protein deubiquitination / regulation of type I interferon production / negative regulation of viral transcription / protein K6-linked ubiquitination / Fc-gamma receptor I complex binding / cellular response to chemical stress / STING mediated induction of host immune responses / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / stress granule disassembly / pyroptotic inflammatory response / negative regulation of NF-kappaB transcription factor activity / FCGR activation / response to type II interferon / protein K63-linked ubiquitination / protein monoubiquitination / complement activation, classical pathway / Role of phospholipids in phagocytosis / proteasomal protein catabolic process / protein K48-linked ubiquitination / antigen binding / protein autoubiquitination / positive regulation of cell cycle / positive regulation of autophagy / antiviral innate immune response / Regulation of innate immune responses to cytosolic DNA / FCGR3A-mediated IL10 synthesis / autophagosome / negative regulation of innate immune response / positive regulation of DNA-binding transcription factor activity / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / P-body / protein destabilization / RING-type E3 ubiquitin transferase / Regulation of actin dynamics for phagocytic cup formation / protein polyubiquitination / cytoplasmic stress granule / Interferon gamma signaling / ubiquitin-protein transferase activity / positive regulation of protein binding / antibacterial humoral response / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of gene expression / cytoplasmic vesicle / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / transcription coactivator activity / positive regulation of viral entry into host cell / protein ubiquitination / ribonucleoprotein complex / innate immune response / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SPRY domain / TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / Modified RING finger domain / U-box domain / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain ...SPRY domain / TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / Modified RING finger domain / U-box domain / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / : / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Immunoglobulin heavy constant gamma 1 / E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.35 Å
AuthorsJames, L.C. / Keeble, A.H. / Rhodes, D.A. / Trowsdale, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structural Basis for Pryspry-Mediated Tripartite Motif (Trim) Protein Function.
Authors: James, L.C. / Keeble, A.H. / Khan, Z. / Rhodes, D.A. / Trowsdale, J.
History
DepositionJun 30, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IG GAMMA-1 CHAIN C
B: 52 KDA RO PROTEIN
D: IG GAMMA-1 CHAIN C
E: 52 KDA RO PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1808
Polymers88,3004
Non-polymers2,8814
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.490, 112.490, 194.609
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13A
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A237 - 443
2111D237 - 443
1121B2 - 184
2121E2 - 184
1131A1444 - 1451
2131D1444 - 1451

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein IG GAMMA-1 CHAIN C / LJ1


Mass: 23547.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 120-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01857
#2: Protein 52 KDA RO PROTEIN / LJ1 / SJOEGREN SYNDROME TYPE A ANTIGEN / SS-A / RO / 52 KDA RIBONUCLEOPROTEIN AUTOANTIGEN RO/SS-A / ...LJ1 / SJOEGREN SYNDROME TYPE A ANTIGEN / SS-A / RO / 52 KDA RIBONUCLEOPROTEIN AUTOANTIGEN RO/SS-A / TRIPARTITE MOTIF PROTEIN 21 / RING FINGER PROTEIN 81


Mass: 20602.201 Da / Num. of mol.: 2 / Fragment: RESIDUES 287-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P19474
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1276.157 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-3-1-4/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.5 Å3/Da / Density % sol: 69 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 10438 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12

-
Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.35→97.59 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 8.825 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.303 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2533 5.19 %RANDOM
Rwork0.215 ---
obs0.217 49869 86.1 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 71.56 Å2
Baniso -1Baniso -2Baniso -3
1--4.242 Å2-2.121 Å20 Å2
2---4.242 Å20 Å2
3---6.363 Å2
Refinement stepCycle: LAST / Resolution: 2.35→97.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 192 172 6590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0226628
X-RAY DIFFRACTIONr_bond_other_d0.0040.023120
X-RAY DIFFRACTIONr_angle_refined_deg2.5881.9819054
X-RAY DIFFRACTIONr_angle_other_deg3.14537281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9985772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51224.228298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.918151034
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8451528
X-RAY DIFFRACTIONr_chiral_restr0.1810.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024984
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02581
X-RAY DIFFRACTIONr_nbd_refined0.2360.22650
X-RAY DIFFRACTIONr_nbd_other0.2410.33043
X-RAY DIFFRACTIONr_nbtor_refined0.3230.24363
X-RAY DIFFRACTIONr_nbtor_other0.4470.517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.381
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4750.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.831.54026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.88326344
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.92433003
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4534.52710
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1658tight positional0.050.05
21B1455tight positional0.060.05
31A96tight positional0.040.05
32D96tight positional0.040.05
12D1658tight thermal0.220.5
22E1455tight thermal0.250.5
31A96tight thermal0.060.5
32D96tight thermal0.060.5
LS refinement shellResolution: 10.45→97.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.454 24
Rwork0.377 528

+
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