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- PDB-6hip: Structure of SPF45 UHM bound to HIV-1 Rev ULM -

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Basic information

Entry
Database: PDB / ID: 6hip
TitleStructure of SPF45 UHM bound to HIV-1 Rev ULM
Components
  • HIV-1 Rev (41-49)
  • Splicing factor 45
KeywordsSPLICING / Splicing factor / viral protein
Function / homology
Function and homology information


alternative mRNA splicing, via spliceosome / host cell nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / mRNA cis splicing, via spliceosome / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation ...alternative mRNA splicing, via spliceosome / host cell nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / mRNA cis splicing, via spliceosome / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA transport / Binding and entry of HIV virion / viral process / mRNA Splicing - Major Pathway / spliceosomal complex / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding / nucleoplasm / identical protein binding
Similarity search - Function
SPF45, RNA recognition motif / Splicing factor 45 / Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / RNA recognition motif domain, eukaryote / RNA recognition motif ...SPF45, RNA recognition motif / Splicing factor 45 / Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHAN / Protein Rev / Splicing factor 45
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPabis, M. / Corsini, L. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Modulation of HIV-1 gene expression by binding of a ULM motif in the Rev protein to UHM-containing splicing factors.
Authors: Pabis, M. / Corsini, L. / Vincendeau, M. / Tripsianes, K. / Gibson, T.J. / Brack-Werner, R. / Sattler, M.
History
DepositionAug 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor 45
B: Splicing factor 45
C: HIV-1 Rev (41-49)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8995
Polymers24,6713
Non-polymers2272
Water5,819323
1
A: Splicing factor 45
C: HIV-1 Rev (41-49)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0613
Polymers13,0382
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-9 kcal/mol
Surface area6050 Å2
MethodPISA
2
B: Splicing factor 45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8382
Polymers11,6331
Non-polymers2041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.210, 63.680, 67.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Splicing factor 45 / 45 kDa-splicing factor / RNA-binding motif protein 17


Mass: 11633.431 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM17, SPF45 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96I25
#2: Protein/peptide HIV-1 Rev (41-49)


Mass: 1404.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: synthetic construct (others) / References: UniProt: P04618*PLUS
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22.5 % (w/v) PEG 3350, 0.1 M HEPES pH 6.0, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99984 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.2→18.49 Å / Num. obs: 64821 / % possible obs: 98.5 % / Redundancy: 7.82 % / Rrim(I) all: 0.17 / Net I/σ(I): 8.18
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 4 % / Num. unique obs: 9278 / Rrim(I) all: 0.647 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PE8

2pe8


Resolution: 1.2→18.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.15 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17502 3242 5.1 %RANDOM
Rwork0.14893 ---
obs0.15022 60832 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 10.526 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.2→18.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 15 323 2048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191908
X-RAY DIFFRACTIONr_bond_other_d0.0030.021878
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9792597
X-RAY DIFFRACTIONr_angle_other_deg1.11534332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65923.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58915352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9561520
X-RAY DIFFRACTIONr_chiral_restr0.1140.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022198
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02430
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_it1.0160.699942
X-RAY DIFFRACTIONr_mcbond_other1.0150.697941
X-RAY DIFFRACTIONr_mcangle_it1.311.0481186
X-RAY DIFFRACTIONr_mcangle_other1.311.051187
X-RAY DIFFRACTIONr_scbond_it1.5170.993966
X-RAY DIFFRACTIONr_scbond_other1.5170.993967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8921.3781398
X-RAY DIFFRACTIONr_long_range_B_refined4.0758.6782433
X-RAY DIFFRACTIONr_long_range_B_other2.8887.0992238
X-RAY DIFFRACTIONr_rigid_bond_restr3.74333786
X-RAY DIFFRACTIONr_sphericity_free32.355570
X-RAY DIFFRACTIONr_sphericity_bonded8.03653994
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 208 -
Rwork0.223 3902 -
obs--85.97 %

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