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- PDB-4pmi: Crystal structure of Rev and Rev-response-element RNA complex -

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Basic information

Entry
Database: PDB / ID: 4pmi
TitleCrystal structure of Rev and Rev-response-element RNA complex
Components
  • Protein Rev
  • Rev-Response-Element RNA
KeywordsRNA binding protein/RNA / protein-RNA complex / helix-loop-helix / HIV / nuclear export / RNA binding protein-RNA complex
Function / homology
Function and homology information


protein localization to nucleoplasm / host cell nucleolus / mRNA transport / viral process / host cell cytoplasm / DNA-binding transcription factor activity / RNA binding
Similarity search - Function
Helix Hairpins - #630 / Anti-repression trans-activator protein, REV protein / REV protein (anti-repression trans-activator protein) / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Protein Rev
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 3.2 Å
AuthorsJayaraman, B. / Crosby, D.C. / Homer, C. / Ribeiro, I. / Mavor, D. / Frankel, A.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM082250 United States
CitationJournal: Elife / Year: 2014
Title: RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex.
Authors: Jayaraman, B. / Crosby, D.C. / Homer, C. / Ribeiro, I. / Mavor, D. / Frankel, A.D.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Feb 13, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rev-Response-Element RNA
B: Protein Rev
C: Protein Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7964
Polymers29,7013
Non-polymers951
Water181
1
A: Rev-Response-Element RNA
B: Protein Rev
C: Protein Rev
hetero molecules

A: Rev-Response-Element RNA
B: Protein Rev
C: Protein Rev
hetero molecules

A: Rev-Response-Element RNA
B: Protein Rev
C: Protein Rev
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,38712
Polymers89,1029
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area16980 Å2
ΔGint-141 kcal/mol
Surface area32400 Å2
MethodPISA
2
A: Rev-Response-Element RNA
B: Protein Rev
C: Protein Rev
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)178,77324
Polymers178,20318
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
crystal symmetry operation18_445-x-3/4,z-1/4,y+1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area37720 Å2
ΔGint-329 kcal/mol
Surface area61030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.300, 165.300, 165.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: RNA chain Rev-Response-Element RNA


Mass: 12939.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#2: Protein Protein Rev / ART/TRS / Anti-repression transactivator / Regulator of expression of viral proteins


Mass: 8380.420 Da / Num. of mol.: 2 / Mutation: L12S, L60R, E47A, truncated at residue 70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Strain: isolate HXB3 / Gene: rev / Production host: Escherichia coli (E. coli) / References: UniProt: P69718
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 6.27 Å3/Da / Density % sol: 80.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 50 mM MES pH 6.0, 50 mM KCl, 1-4% PEG 4000,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionNumber: 200271 / Rmerge(I) obs: 0.146 / Χ2: 2.33 / D res high: 5.55 Å / Num. obs: 13162 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
24.8345.8513110.032
17.5624.8327510.045
14.3417.5634810.06
12.4214.3440910.069
11.1112.4248310.077
10.1411.1151710.084
9.3910.1456110.101
8.789.3961010.112
8.288.7864410.164
7.858.2868110.165
7.497.8571910.249
7.177.4975910.321
6.897.1776910.401
6.646.8981710.521
6.416.6483810.647
6.216.4187510.793
6.026.2190811.106
5.856.0293311.184
5.75.8595211.411
5.555.793311.462
ReflectionResolution: 3.2→45.85 Å / Num. obs: 13246 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 25.9 % / Biso Wilson estimate: 91.889 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.117 / Χ2: 0.978 / Net I/σ(I): 23.47 / Num. measured all: 343444
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allRmerge(I) obs
3.2-3.3115.90.3781.7414120178917512.08998.36
3.28-3.370.5571.5917956177117702.12199.92.014
3.37-3.470.8392.5919624169516941.54799.91.478
3.47-3.580.8543.1419194164816481.3481001.288
3.58-3.70.9194.3918205157015690.98799.90.943
3.7-3.820.9455.2518324157615760.791000.755
3.82-3.970.9496.5517199148714840.67299.80.642
3.97-4.130.988.6316534141314130.4551000.435
4.13-4.320.98510.0116012137213720.3851000.368
4.32-4.530.99314.6515334131713170.231000.22
4.53-4.770.99518.5514800126912690.1771000.169
4.77-5.060.9962114193115511550.1561000.149
5.06-5.410.99724.0425897112211220.221000.215
5.41-5.840.99724.324212103610360.2011000.197
5.84-6.40.99830.65222689509500.1481000.145
6.4-7.160.99936.59200608608600.1121000.11
7.16-8.260.99953.26176267617610.0691000.068
8.26-10.120.99962.9144786416410.0531000.052
10.12-14.310.99972.58115524994990.0441000.043
14.31-45.850.99978.1459852762680.03997.10.038

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIXrefinement
Cootmodel building
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lph, 1etf
Resolution: 3.2→45.846 Å / FOM work R set: 0.8468 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 1325 10.01 %
Rwork0.1928 11917 -
obs0.1946 13242 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.85 Å2 / Biso mean: 114.71 Å2 / Biso min: 65.52 Å2
Refinement stepCycle: final / Resolution: 3.2→45.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 849 5 1 1717
Biso mean--153.79 112.73 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021832
X-RAY DIFFRACTIONf_angle_d0.3942668
X-RAY DIFFRACTIONf_chiral_restr0.02321
X-RAY DIFFRACTIONf_plane_restr0.002198
X-RAY DIFFRACTIONf_dihedral_angle_d11.911828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2002-3.32830.30141410.27881268140998
3.3283-3.47970.29771440.249312961440100
3.4797-3.66310.22831430.213912871430100
3.6631-3.89250.22441450.223912981443100
3.8925-4.19290.24241430.206412991442100
4.1929-4.61450.18871480.174413261474100
4.6145-5.28140.17541480.172313271475100
5.2814-6.65070.22431500.202713591509100
6.6507-45.85070.18731630.16714571620100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.96280.664-4.73642.9521-0.53575.05490.51620.23330.00020.77980.2765-0.9213-0.68590.8554-0.81660.8587-0.17810.02381.3614-0.30640.7596-36.6385-21.184916.8382
28.6077-1.0455-6.40856.61232.4524.9332-0.277-1.4189-0.30890.42470.4376-0.5536-0.42950.0826-0.10770.8460.14010.15441.6506-0.57431.9737-13.0085-34.69278.5952
37.1021-4.6974-3.17728.1061.73731.45370.084-0.29060.51870.27310.5792-1.289-0.31410.5393-0.61190.79040.0463-0.05241.2293-0.25020.6216-36.0927-21.044920.3169
44.8165-0.21132.90960.8087-1.87875.90160.94561.4056-0.2351-0.14-0.23320.2273-0.4873-1.0491-0.80830.64730.2545-0.17761.583-0.56361.2053-46.1605-38.4943-6.2728
59.79188.04625.06387.4953.31263.917-0.48212.83233.8022-1.56422.00050.5594-1.07963.1964-1.07261.0398-0.45290.47261.7411-0.19771.666-29.2858-24.9921-0.2573
62.3974-3.37080.79715.66051.31345.607-0.11810.5987-1.23530.15990.34820.53050.16360.8768-0.2840.66190.06120.25561.2575-0.45371.2163-34.898-36.29874.1596
79.93721.8573-0.56264.5668-3.37087.3562-0.14871.0583-1.5694-0.18660.97830.65640.8054-0.427-0.89140.6639-0.17250.27571.3358-0.23641.3699-50.6644-40.64748.8384
84.91311.3067-0.22823.8483-2.66031.92340.057-2.4735-2.143-0.3799-1.2082-0.2664-0.38070.40030.53910.86290.0765-0.07271.34310.01470.8018-38.2656-34.423725.4474
99.6977-0.33967.72434.6522.131110.0776-0.205-0.50890.15040.0782-0.02490.3058-0.3739-0.34810.16160.53510.06980.22910.9684-0.04221.0017-44.3764-29.506413.6319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 48 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 70 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 82 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 24 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 34 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 63 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 13 through 25 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 26 through 34 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 35 through 64 )C0

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