[English] 日本語
Yorodumi
- PDB-3zo0: Mouse IgG2a in complex with mouse TRIM21 PRYSPRY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zo0
TitleMouse IgG2a in complex with mouse TRIM21 PRYSPRY
Components
  • E3 UBIQUITIN-PROTEIN LIGASE TRIM21
  • IG GAMMA-2A CHAIN C REGION, A ALLELE
KeywordsIMMUNE SYSTEM/LIGASE / IMMUNE SYSTEM-LIGASE COMPLEX
Function / homology
Function and homology information


negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / regulation of viral entry into host cell / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / stress granule disassembly / immunoglobulin complex, circulating / immunoglobulin receptor binding / negative regulation of NF-kappaB transcription factor activity / response to type II interferon ...negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / regulation of viral entry into host cell / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / stress granule disassembly / immunoglobulin complex, circulating / immunoglobulin receptor binding / negative regulation of NF-kappaB transcription factor activity / response to type II interferon / protein monoubiquitination / protein K63-linked ubiquitination / complement activation, classical pathway / protein autoubiquitination / positive regulation of autophagy / positive regulation of cell cycle / antigen binding / negative regulation of innate immune response / autophagosome / P-body / protein destabilization / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / antibacterial humoral response / positive regulation of protein binding / regulation of protein localization / cytoplasmic vesicle / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / ribonucleoprotein complex / innate immune response / protein kinase binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
SPRY domain / TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger ...SPRY domain / TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / : / 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. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / alpha-D-mannopyranose / Ig gamma-2A chain C region, A allele / E3 ubiquitin-protein ligase TRIM21
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.99 Å
AuthorsJames, L.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Trim21 is an Igg Receptor that is Structurally, Thermodynamically, and Kinetically Conserved.
Authors: Keeble, A.H. / Khan, Z. / Forster, A. / James, L.C.
History
DepositionFeb 19, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionMay 22, 2013ID: 2VOL
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IG GAMMA-2A CHAIN C REGION, A ALLELE
B: E3 UBIQUITIN-PROTEIN LIGASE TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0965
Polymers44,6382
Non-polymers1,4583
Water3,405189
1
A: IG GAMMA-2A CHAIN C REGION, A ALLELE
B: E3 UBIQUITIN-PROTEIN LIGASE TRIM21
hetero molecules

A: IG GAMMA-2A CHAIN C REGION, A ALLELE
B: E3 UBIQUITIN-PROTEIN LIGASE TRIM21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,19210
Polymers89,2754
Non-polymers2,9176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area6730 Å2
ΔGint-37.8 kcal/mol
Surface area44310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.458, 186.185, 124.875
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-2075-

HOH

21A-2086-

HOH

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein IG GAMMA-2A CHAIN C REGION, A ALLELE / IGG2A / IMMUNOGLOBULIN HEAVY CHAIN GAMMA POLYPEPTIDE


Mass: 23849.016 Da / Num. of mol.: 1 / Fragment: FC, RESIDUES 120-327 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / References: UniProt: P01863
#2: Protein E3 UBIQUITIN-PROTEIN LIGASE TRIM21 / TRIM21 / 52 KDA RO PROTEIN / 52 KDA RIBONUCLEOPROTEIN AUTOANTIGEN RO/SS-A / RO(SS-A) / SJOEGREN ...TRIM21 / 52 KDA RO PROTEIN / 52 KDA RIBONUCLEOPROTEIN AUTOANTIGEN RO/SS-A / RO(SS-A) / SJOEGREN SYNDROME TYPE A ANTIGEN / SS-A / TRIPARTITE MOTIF-CONTAINING PROTEIN 21


Mass: 20788.518 Da / Num. of mol.: 1 / Fragment: RESIDUES 291-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q62191, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

-
Sugars , 3 types, 3 molecules

#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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-4/a4-b1_b4-c1_c6-d1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 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.: 1
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

-
Non-polymers , 1 types, 189 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.44 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→44 Å / Num. obs: 36717 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8

-
Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.99→44.15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.68 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25251 1798 5 %RANDOM
Rwork0.18132 ---
obs0.18474 34168 97.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.524 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.99→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 96 189 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193311
X-RAY DIFFRACTIONr_bond_other_d0.0020.023035
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.9694516
X-RAY DIFFRACTIONr_angle_other_deg2.0463.0016980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8645386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91424.342152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.57515533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7791516
X-RAY DIFFRACTIONr_chiral_restr0.1920.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213640
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02760
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6433.3151550
X-RAY DIFFRACTIONr_mcbond_other5.643.3121549
X-RAY DIFFRACTIONr_mcangle_it6.3214.9541934
X-RAY DIFFRACTIONr_mcangle_other6.3374.9591935
X-RAY DIFFRACTIONr_scbond_it6.3473.841761
X-RAY DIFFRACTIONr_scbond_other6.3463.8411762
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1235.5292583
X-RAY DIFFRACTIONr_long_range_B_refined7.49328.5963868
X-RAY DIFFRACTIONr_long_range_B_other7.47728.4483819
X-RAY DIFFRACTIONr_rigid_bond_restr11.75836346
X-RAY DIFFRACTIONr_sphericity_free29.817563
X-RAY DIFFRACTIONr_sphericity_bonded14.66456377
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 143 -
Rwork0.215 2370 -
obs--94.12 %
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)
10.05870.1378-0.07740.3467-0.1250.58430.02190.01230.01480.04520.01440.03030.0195-0.0709-0.03640.02350.00110.0140.0335-0.00720.036215.721514.3752-20.5431
20.3958-0.06240.10060.69350.17820.8381-0.0235-0.0235-0.02090.0757-0.01950.03140.0573-0.03960.0430.0118-0.00050.00970.0417-0.00790.051315.653233.50965.1796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A237 - 1451
2X-RAY DIFFRACTION2B7 - 186

+
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