[English] 日本語
Yorodumi
- PDB-9c75: The crystal structure of HIV-1 Rev Response Element Stem-Loop II ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c75
TitleThe crystal structure of HIV-1 Rev Response Element Stem-Loop II G34U mutant in complex with a Fab
Components
  • BL3-6 Fab Heavy Chain
  • BL3-6 Fab Light Chain
  • Rev Response Element
KeywordsRNA/IMMUNE SYSTEM / HIV-1 / Replication / Fab / Chaperone / Rev response element / RNA / RNA-IMMUNE SYSTEM complex
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsOjha, M. / Koirala, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170660-01/SUBK00019302 United States
CitationJournal: To Be Published
Title: The crystal structure of HIV-1 Rev Response Element Stem-Loop II G34U mutant in complex with a Fab
Authors: Ojha, M. / Koirala, D.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: BL3-6 Fab Heavy Chain
L: BL3-6 Fab Light Chain
R: Rev Response Element


Theoretical massNumber of molelcules
Total (without water)71,3843
Polymers71,3843
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.878, 105.014, 186.603
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Antibody BL3-6 Fab Heavy Chain


Mass: 24766.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody BL3-6 Fab Light Chain


Mass: 23394.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: RNA chain Rev Response Element


Mass: 23222.867 Da / Num. of mol.: 1 / Fragment: Stem-Loop II / Mutation: G34U / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: GenBank: 902798
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M NaCl, 0.1M Tris pH 8.0, 12.5% polyvinylpyrrolidone, 10% PEG 4000
PH range: 7-8.5

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 3.04→34.64 Å / Num. obs: 17512 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.076 / Rrim(I) all: 0.198 / Net I/σ(I): 7.1
Reflection shellResolution: 3.042→3.095 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.518 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 855 / CC1/2: 0.383 / Rpim(I) all: 1.028 / Rrim(I) all: 2.723 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04→34.64 Å / SU ML: 0.6602 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.8057
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 849 4.85 %
Rwork0.2055 16639 -
obs0.2079 17488 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 135.2 Å2
Refinement stepCycle: LAST / Resolution: 3.04→34.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 1540 0 0 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915126
X-RAY DIFFRACTIONf_angle_d1.22627308
X-RAY DIFFRACTIONf_chiral_restr0.0591879
X-RAY DIFFRACTIONf_plane_restr0.0113663
X-RAY DIFFRACTIONf_dihedral_angle_d16.68221339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.230.48131450.38622722X-RAY DIFFRACTION99.69
3.23-3.480.32971230.29142737X-RAY DIFFRACTION99.93
3.48-3.830.32191480.24042738X-RAY DIFFRACTION99.97
3.83-4.390.24011400.1962767X-RAY DIFFRACTION99.97
4.39-5.520.19661170.17162820X-RAY DIFFRACTION99.97
5.52-34.640.22121760.17082855X-RAY DIFFRACTION99.31
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)
12.0028831199-1.205322261711.907669153571.50840059423-2.196353614715.015192931010.322743165732-0.384838416442-0.4253030985510.1228630526630.3342822027330.0558126407114-0.2376111237470.347048846029-0.5435874567840.734798408706-0.1785475635050.0307573473490.999929671053-0.05106353963370.88087072292530.1033419064-1.0385318944133.2888440615
22.697523864910.9509753271691.144914374963.287482288690.4687584280751.63729127140.121545056706-0.4191910765930.1533347466590.24323449224-0.4373934524020.7996521805220.02558465707890.3949679484740.1439665829480.831798850165-0.269633448846-0.1156108349811.145251134820.1712971595791.0154324502430.4134325602-13.247732450148.9527660115
31.42326547897-0.242895844392-0.6052527226753.149882663132.814402940982.30223773161-0.2814867534-0.761950296546-0.6538065785770.252682931296-0.181069852948-0.5824174947890.4214807063082.617298750760.1037113729350.823940303467-0.378954540283-0.2923745032541.120298721740.5816482752421.3269174773337.5722697661-20.310698968452.6825235404
44.40235006934-1.2838388175-0.3645848978042.41028114870.9436245363284.756609291560.588540948006-1.162623691950.2706227965430.285202364011-0.4265107174110.886163907814-0.314850092593-0.267069535265-0.1458292029050.870062427743-0.0827167890750.03327212506091.18403227232-0.1665343382650.9332761655478.32758100029-1.0919535655829.1503306612
55.868624929481.91989975678-1.881533027643.312359899120.1972346762863.245541047710.266945684028-0.313313318332-0.255019667414-0.19460627598-0.010684464586-0.01665836100220.07917498356840.175951137638-0.2166175014460.67883905495-0.032826324782-0.03600939283220.649723110654-0.1007125780.75146145459513.0187984712-1.7406267003521.707291794
60.935966715218-1.311682672960.9121570885632.05255567742-0.3099941255684.14731256630.456035888253-1.84638076724-0.7776190790170.785789587331-0.1517712070320.234645369930.120512804982-0.547300844345-0.2444940478020.859610913456-0.390107601975-0.01475118608611.593534171170.2746128092561.0785313237910.5202569425-16.521288185342.7009574652
71.623163269052.120855390370.6522341134623.0502320084-0.451168389762.846668226440.544429158988-1.1728505729-0.4962386908811.27998791685-0.2732519471170.176784697279-0.351247779647-0.123824241168-0.02836005968771.30279916808-0.2339639614210.04264579913521.766541365780.2040272028861.1522620824722.3409766919-11.795207767758.0891823134
83.03832802585-0.0258200335512.482401915293.398299278240.3404451659563.084005526770.236367628603-1.519116522190.003094146597020.9121070971920.08454440950660.586184772513-0.211329111608-1.94118983555-0.384409467381.25721406757-0.1959038468720.1695568558221.818202267140.1992620215161.110208016919.1889381966-11.203732450559.8537471163
93.535558748323.662956171310.4107707138363.25381883737-0.2133677872182.00483972323-3.313449537822.17671606306-1.570110814091.91980985041.14558053535-0.866859298674-0.3864775406220.526603930960.4012496823283.41583569716-0.1121222289510.7061353094241.44939667467-0.5753013721841.3878405214426.782315592638.6904390548-18.1964705823
102.30505075941-1.66503091949-2.141517919216.189068629951.443810662432.69591930812-0.356993706556-2.303806741770.631599678349-2.850413428971.65746289194-2.609582891130.2603426384310.222780963726-0.6491267855852.79983826542-0.4722552891361.06387476032.15927921338-0.4713363191733.0349080390846.725815098834.1048424889-19.6755736159
112.082979548260.0944741591664-1.209808587410.032772136523-0.08012505009050.724602598746-1.253018632741.137690167520.298226543334-1.979631234710.8698739213911.28105285796-1.54361744563-1.212318726550.141699814793.40994816255-0.1420613178490.5706901470771.69181659229-0.150508612241.8197067057824.432221516925.6979834724-23.5684564875
12-0.4476652781960.700089309799-0.05263775506132.33548852904-1.747988620811.451907092950.4559110371420.17191369819-0.01655373369750.903352515568-0.6006438452091.00843988026-1.350048193791.092590525140.1528292220961.19822072609-0.1733158988790.2249246363550.892556691889-0.2057776022811.0986703301719.659139296819.8038115157-2.8229067212
130.0317414243480.161612623555-0.1982049280010.256712275707-0.2618528197771.172744781280.102501431993-0.173815185307-0.155112408391.5065119178-0.1557312129070.205676932731-1.91984693803-1.82857961755-0.6206667048522.66037082842-0.1509371567670.2066197088120.9284327630580.2690443343321.7415768063821.509774462650.3646883281-9.82919157238
142.8367240794-0.418937306011-0.6556865108982.637803826071.04348116847.298619703580.3329562236450.609410801036-0.1621288096140.3241099356450.666351556596-1.374121946830.1542460100562.03570509676-0.5717735122480.780348701649-0.0982474135689-0.06523865178091.02932087711-0.1263897147290.84093433367438.21180489732.9603187850727.1531184308
154.108075998580.338704697320.9398021352171.75638651757-1.795877330533.101715385660.2570845862190.347009816016-0.2110089573840.0839921595025-0.5650467659620.0281264756561-0.5782092028750.8884385375370.2738996619220.763113721897-0.1035839474480.03177153429790.919329981265-0.2147538777740.79600119289329.46387662157.083196758419.4718031228
163.084180375480.0397082836572-1.19463739043.24485337679-0.6960681478834.922687698870.5370722005140.05191313659560.1592519305280.498496600469-0.637368834080.309566126464-0.0785384055489-0.0392551530421-0.02319446269830.90356437146-0.3160505313770.06093874972731.23925872744-0.1394744787710.863452309635.745434623111.639870969322.6663919092
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 87 through 143 )HA87 - 14385 - 141
22chain 'H' and (resid 144 through 197 )HA144 - 197142 - 195
33chain 'H' and (resid 198 through 228 )HA198 - 228196 - 226
44chain 'L' and (resid 1 through 19 )LB1 - 191 - 19
55chain 'L' and (resid 20 through 103 )LB20 - 10320 - 103
66chain 'L' and (resid 104 through 116 )LB104 - 116104 - 116
77chain 'L' and (resid 117 through 151 )LB117 - 151117 - 151
88chain 'L' and (resid 152 through 215 )LB152 - 215152 - 215
99chain 'R' and (resid 1 through 15 )RC1 - 15
1010chain 'R' and (resid 16 through 35 )RC16 - 35
1111chain 'R' and (resid 36 through 40 )RC36 - 40
1212chain 'R' and (resid 41 through 65 )RC41 - 65
1313chain 'R' and (resid 66 through 72 )RC66 - 72
1414chain 'H' and (resid 3 through 26 )HA3 - 261 - 24
1515chain 'H' and (resid 27 through 63 )HA27 - 6325 - 61
1616chain 'H' and (resid 64 through 86 )HA64 - 8662 - 84

+
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://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