[English] 日本語
Yorodumi
- PDB-8uo6: HIV-1 Rev Response Element (RRE) Stem-Loop II (SLII) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uo6
TitleHIV-1 Rev Response Element (RRE) Stem-Loop II (SLII)
ComponentsHIV-1 Rev Response Element Stem-Loop II with tRNA scaffold
KeywordsRNA / Non-coding RNA / HIV / Nuclear Export / RRE / viral RNA
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHIV whole-genome vector AA1305#18 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsTipo, J. / Gottipati, K. / Choi, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI187856 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site.
Authors: Tipo, J. / Gottipati, K. / Slaton, M. / Gonzalez-Gutierrez, G. / Choi, K.H.
History
DepositionOct 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold
B: HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold


Theoretical massNumber of molelcules
Total (without water)86,6832
Polymers86,6832
Non-polymers00
Water00
1
A: HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold


Theoretical massNumber of molelcules
Total (without water)43,3421
Polymers43,3421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold


Theoretical massNumber of molelcules
Total (without water)43,3421
Polymers43,3421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.782, 81.314, 81.372
Angle α, β, γ (deg.)90.000, 99.140, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: A / End label comp-ID: A / Auth seq-ID: 1 - 7 / Label seq-ID: 1 - 7

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.747372200546, 0.10026959512, -0.65679586033), (-0.0763694275933, -0.994959043273, -0.0649939438615), (-0.660001897255, 0.00158445705313, 0.751262261208)Vector: 22. ...NCS oper: (Code: given
Matrix: (-0.747372200546, 0.10026959512, -0.65679586033), (-0.0763694275933, -0.994959043273, -0.0649939438615), (-0.660001897255, 0.00158445705313, 0.751262261208)
Vector: 22.6737929428, 2.59151013292, -3.31835187928)

-
Components

#1: RNA chain HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold


Mass: 43341.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 52_53insG
Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others)
Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM SPG (mixture of succinic acid, sodium dihydrogen phosphate, and glycine in a 2:7:7 molar ratio), 20-24% polyethylene glycol-6000, and 200 mM sodium fluoride
PH range: 7.0-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→57.2 Å / Num. obs: 12674 / % possible obs: 88.5 % / Redundancy: 4 % / Biso Wilson estimate: 66.82 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.05 / Rrim(I) all: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 2.85→3.2 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 635 / CC1/2: 0.487 / Rpim(I) all: 0.72

-
Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→57.15 Å / SU ML: 0.3332 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 605 4.78 %
Rwork0.2314 12061 -
obs0.2326 12666 61.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.73 Å2
Refinement stepCycle: LAST / Resolution: 2.85→57.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5742 0 0 5742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266420
X-RAY DIFFRACTIONf_angle_d0.756110014
X-RAY DIFFRACTIONf_chiral_restr0.03781340
X-RAY DIFFRACTIONf_plane_restr0.0046268
X-RAY DIFFRACTIONf_dihedral_angle_d19.41043210
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 11.4834766904 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.130.4228300.3367551X-RAY DIFFRACTION11.33
3.13-3.590.31611000.27032135X-RAY DIFFRACTION43.78
3.59-4.520.30022350.27574446X-RAY DIFFRACTION90.61
4.52-57.150.21692400.19884929X-RAY DIFFRACTION99.08
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)
11.79335687119-0.757303848790.2018375411532.00017833993-0.3029373823550.680701961309-0.20503969894-0.618217429668-0.2210988125991.027411931670.1693697081740.464336181223-0.109841734486-0.247182099512-0.02100533742340.580450396190.3243004203470.08634181455210.352361774755-0.2050529047181.0071507467-12.97548060211.117487752221.6318131459
20.6441224891370.6911397186720.5834435691043.371490139372.022619292371.27835506001-0.294453760567-0.62666568699-0.1582791300390.878685067870.319288083722-0.2533527288041.197357925430.606141088683-0.08623591187770.8500236522810.398093869631-0.08849085804551.240635241630.03286890988120.496579214204-18.37780409951.432542355933.6669332105
32.31516394967-0.665343169136-0.04058939535682.665209929470.2963353390322.61925797929-0.165576871492-0.0986811561999-0.3718660321870.563878978611-0.168407045346-0.01620986452420.13925372360.1138456272220.1658621338390.222114042590.1611134523390.001753318440780.4394220985710.007533946479150.962420104439-6.999590850140.86214572665410.1631733643
41.90138701894-2.025247283330.6073474044032.7997939758-0.03527379871440.68782780619-0.0485066751851-0.267325402743-0.130757221540.9722516755960.5518258833340.596348222685-0.236088969578-0.554622134145-0.4493052364930.6956707611330.3967134680420.05944677417710.9349787666790.1789441197120.6998696441122.7219993907-8.8128130966920.5271228005
54.588430648112.632395683751.021673579425.55815999682-1.937316797081.788533540440.235493097679-0.8668332899630.4442579148831.42831732360.1095424941680.105001976416-1.03431518983-0.545792083006-0.3384720503571.006103580540.1331645139350.1208196442631.31559393930.1823987244410.91143860003518.5199106321-49.463435593634.6085053765
61.90307504821-0.3575963675820.8368064198371.453024445280.2802742988090.684746307763-0.244261101628-0.561049640199-0.3261266191340.6475348470710.305770717761-0.03168588920940.219720587191-0.213607214502-0.09546908335440.2730922380520.523524847650.245265111640.8569284058210.244145028510.79168046656819.16252967750.5149604305649.94803023397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 40 )AA1 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 92 )AA41 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 134 )AA93 - 134
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 40 )BB1 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 91 )BB41 - 91
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 134 )BB92 - 134

+
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://pdbjlvh1.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