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- PDB-4b3n: Crystal structure of rhesus TRIM5alpha PRY/SPRY domain -

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Basic information

Entry
Database: PDB / ID: 4b3n
TitleCrystal structure of rhesus TRIM5alpha PRY/SPRY domain
ComponentsMALTOSE-BINDING PERIPLASMIC PROTEIN, TRIPARTITE MOTIF-CONTAINING PROTEIN 5
KeywordsSUGAR BINDING PROTEIN/LIGASE / SUGAR BINDING PROTEIN-LIGASE COMPLEX / SUGAR BINDING PROTEIN-LIGASE CHIMERA
Function / homology
Function and homology information


regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / negative regulation of viral transcription / pattern recognition receptor activity / negative regulation of viral genome replication / detection of maltose stimulus / maltose transport complex / carbohydrate transport ...regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / negative regulation of viral transcription / pattern recognition receptor activity / negative regulation of viral genome replication / detection of maltose stimulus / maltose transport complex / carbohydrate transport / protein K63-linked ubiquitination / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of autophagy / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / activation of innate immune response / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / P-body / RING-type E3 ubiquitin transferase / autophagy / positive regulation of DNA-binding transcription factor activity / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / outer membrane-bounded periplasmic space / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / positive regulation of MAPK cascade / periplasmic space / innate immune response / DNA damage response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
SPRY domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain ...SPRY domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / 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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Bacterial extracellular solute-binding protein / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Tripartite motif-containing protein 5
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MACACA MULATTA (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsYang, H. / Ji, X. / Zhao, Q. / Xiong, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Insight Into HIV-1 Capsid Recognition by Rhesus Trim5Alpha
Authors: Yang, H. / Ji, X. / Zhao, G. / Ning, J. / Zhao, Q. / Aiken, C. / Gronenborn, A.M. / Zhang, P. / Xiong, Y.
History
DepositionJul 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, TRIPARTITE MOTIF-CONTAINING PROTEIN 5
B: MALTOSE-BINDING PERIPLASMIC PROTEIN, TRIPARTITE MOTIF-CONTAINING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,6146
Polymers134,5392
Non-polymers1,0754
Water79344
1
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, TRIPARTITE MOTIF-CONTAINING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8073
Polymers67,2691
Non-polymers5382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MALTOSE-BINDING PERIPLASMIC PROTEIN, TRIPARTITE MOTIF-CONTAINING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8073
Polymers67,2691
Non-polymers5382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.837, 98.733, 110.332
Angle α, β, γ (deg.)90.00, 122.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MALTOSE-BINDING PERIPLASMIC PROTEIN, TRIPARTITE MOTIF-CONTAINING PROTEIN 5 / MBP / MMBP / MALTODEXTRIN-BINDING PROTEIN / TRIM5ALPHA


Mass: 67269.273 Da / Num. of mol.: 2
Fragment: MBP RESIDUES 27-395, TRIM5ALPHA PRY/SPRY DOMAIN RESIDUES 275-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli), (gene. exp.) MACACA MULATTA (Rhesus monkey)
Plasmid: PMAT9S / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9, UniProt: Q0PF16
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 6.2
Details: 6% (W/V) GLUCOSE, 6% (W/V) TREHALOSE, 100 MM MES PH 6.2 AND 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 30, 2012
Details: HORIZONTAL FOCUSING SAGITTAL BEND SECOND MONO CRYSTAL AND VERTICALLY FOCUSING MIRROR
RadiationMonochromator: CRYOGENICALLY COOLED DOUBLE CRYSTAL MONOCHROMETER
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 22400 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.69
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.39 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ANF, 2VOL

1anf

2vol
PDB Unreleased entry


Resolution: 3.3→49.42 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.875 / SU B: 59.229 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.546 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24843 1135 5.1 %RANDOM
Rwork0.20788 ---
obs0.21 21248 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.292 Å2
Baniso -1Baniso -2Baniso -3
1-3.43 Å20 Å20.18 Å2
2---3.2 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 3.3→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8746 0 70 44 8860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.029042
X-RAY DIFFRACTIONr_bond_other_d0.0050.028498
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9612285
X-RAY DIFFRACTIONr_angle_other_deg1.053319623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23151107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13424.788401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.552151473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0091532
X-RAY DIFFRACTIONr_chiral_restr0.0730.21343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110182
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022042
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 78 -
Rwork0.297 1484 -
obs--91.03 %
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)
12.9047-0.1592-1.12563.37370.27442.1725-0.43110.0148-0.3735-0.05540.2608-0.2420.53050.57330.17030.28250.02460.08990.4886-0.08060.08779.844534.9991-34.7499
26.25871.86870.09054.2816-0.79273.3822-0.48520.3037-0.4997-0.19650.4124-0.32780.14580.39250.07280.1876-0.03040.08680.3762-0.02860.1663-18.48338.5339-17.3211
33.79240.86590.08723.0303-0.65293.7377-0.26780.296-0.38560.04450.11980.25830.601-0.19510.1480.1508-0.10670.10470.3059-0.01980.2205-30.252635.6527-13.5706
41.6069-0.10940.26713.28250.43.6826-0.05210.21640.357-0.29310.16980.087-0.79510.1124-0.11760.1964-0.08850.03230.31680.04280.233123.280370.3168-15.5968
54.88721.01111.70132.210.85064.1907-0.1220.14390.0835-0.02230.2848-0.0068-0.80090.1809-0.16290.1757-0.05330.04940.2851-0.05630.028620.733867.739920.3659
64.0811.58721.19124.49310.08993.92590.1072-0.09920.28470.51550.16870.05-0.54910.2375-0.2760.24070.00290.0780.2589-0.08040.073218.935969.446431.6212
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 371
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION2A372 - 1323
4X-RAY DIFFRACTION3A1324 - 1493
5X-RAY DIFFRACTION3A600
6X-RAY DIFFRACTION4B5 - 371
7X-RAY DIFFRACTION4B500
8X-RAY DIFFRACTION5B372 - 1384
9X-RAY DIFFRACTION6B1385 - 1493
10X-RAY DIFFRACTION6B600

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