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- PDB-3zo0: Mouse IgG2a in complex with mouse TRIM21 PRYSPRY -

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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 / protein K27-linked ubiquitination / suppression of viral release by host / KEAP1-NFE2L2 pathway / protein K6-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of viral transcription / stress granule disassembly ...negative regulation of protein deubiquitination / Regulation of innate immune responses to cytosolic DNA / regulation of viral entry into host cell / protein K27-linked ubiquitination / suppression of viral release by host / KEAP1-NFE2L2 pathway / protein K6-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of viral transcription / stress granule disassembly / Fc-gamma receptor I complex binding / negative regulation of NF-kappaB transcription factor activity / immunoglobulin complex, circulating / IgG immunoglobulin complex / response to type II interferon / immunoglobulin receptor binding / pyroptosis / protein monoubiquitination / protein K63-linked ubiquitination / autophagosome / protein K48-linked ubiquitination / protein autoubiquitination / positive regulation of cell cycle / positive regulation of autophagy / complement activation, classical pathway / antigen binding / negative regulation of innate immune response / proteasomal protein catabolic process / P-body / protein destabilization / RING-type E3 ubiquitin transferase / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of protein binding / antibacterial humoral response / cytoplasmic vesicle / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / protein ubiquitination / cell cycle / ribonucleoprotein complex / innate immune response / protein kinase binding / protein homodimerization activity / DNA binding / extracellular space / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / SPRY 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 ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / SPRY 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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)

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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 / 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 / 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

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Non-polymers , 1 types, 189 molecules

#6: Water ChemComp-HOH / water / Water


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

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

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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

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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

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