[English] 日本語
Yorodumi
- PDB-5jw9: The Crystal Structure of ELL2 Oclludin Domain and AFF4 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jw9
TitleThe Crystal Structure of ELL2 Oclludin Domain and AFF4 peptide
Components
  • AF4/FMR2 family member 4
  • RNA polymerase II elongation factor ELL2
KeywordsPROTEIN BINDING / Occludin domain / HIV transcription / P-TEFb
Function / homology
Function and homology information


super elongation complex / snRNA transcription by RNA polymerase II / spermatid development / RNA polymerase II transcribes snRNA genes / cis-regulatory region sequence-specific DNA binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / response to endoplasmic reticulum stress / transcription elongation factor complex ...super elongation complex / snRNA transcription by RNA polymerase II / spermatid development / RNA polymerase II transcribes snRNA genes / cis-regulatory region sequence-specific DNA binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / response to endoplasmic reticulum stress / transcription elongation factor complex / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / euchromatin / fibrillar center / regulation of gene expression / nucleoplasm
Similarity search - Function
AF-4 proto-oncoprotein N-terminal region / AF4/FMR2 family / AF4 interaction motif / AF4/FMR2, C-terminal homology domain / AF4 interaction motif / AFF4, C-terminal homology domain / RNA polymerase II elongation factor ELL, N-terminal / RNA polymerase II elongation factor ELL / Occludin/ELL (OCEL) domain profile. / Occludin homology domain ...AF-4 proto-oncoprotein N-terminal region / AF4/FMR2 family / AF4 interaction motif / AF4/FMR2, C-terminal homology domain / AF4 interaction motif / AFF4, C-terminal homology domain / RNA polymerase II elongation factor ELL, N-terminal / RNA polymerase II elongation factor ELL / Occludin/ELL (OCEL) domain profile. / Occludin homology domain / ELL/occludin family / Occludin homology domain / E3 ubiquitin-protein ligase ELL-like / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
RNA polymerase II elongation factor ELL2 / AF4/FMR2 family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.003 Å
AuthorsQi, S. / Hurley, J.H.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for ELL2 and AFF4 activation of HIV-1 proviral transcription.
Authors: Qi, S. / Li, Z. / Schulze-Gahmen, U. / Stjepanovic, G. / Zhou, Q. / Hurley, J.H.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AF4/FMR2 family member 4
B: RNA polymerase II elongation factor ELL2


Theoretical massNumber of molelcules
Total (without water)21,5522
Polymers21,5522
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-21 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.641, 57.422, 61.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein AF4/FMR2 family member 4 / ALL1-fused gene from chromosome 5q31 protein / Protein AF-5q31 / Major CDK9 elongation factor- ...ALL1-fused gene from chromosome 5q31 protein / Protein AF-5q31 / Major CDK9 elongation factor-associated protein


Mass: 6629.030 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFF4, AF5Q31, MCEF, HSPC092 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHB7
#2: Protein RNA polymerase II elongation factor ELL2


Mass: 14923.333 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELL2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00472
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2M NaCl, 10mM MgCl, 0.3M Na3 Citrate, 0.2M Na Thiocyanate, 0.1M Hepes 7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2016
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13052 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 31.72 Å2 / Rmerge(I) obs: 0.142 / Net I/av σ(I): 19.5 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2-2.0712.71100
2.07-2.1513.911000.807
2.15-2.2514.311000.663
2.25-2.3714.411000.474
2.37-2.5214.411000.341
2.52-2.7114.311000.273
2.71-2.9914.311000.198
2.99-3.4214.111000.137
3.42-4.3113.911000.105
4.31-5013.2199.90.079

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
SHELXphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.003→41.92 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.08
RfactorNum. reflection% reflection
Rfree0.2483 539 4.14 %
Rwork0.197 --
obs0.1991 13004 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.6 Å2 / Biso mean: 45.1865 Å2 / Biso min: 16.24 Å2
Refinement stepCycle: final / Resolution: 2.003→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 0 97 1376
Biso mean---41.08 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031343
X-RAY DIFFRACTIONf_angle_d0.5691819
X-RAY DIFFRACTIONf_chiral_restr0.033183
X-RAY DIFFRACTIONf_plane_restr0.003238
X-RAY DIFFRACTIONf_dihedral_angle_d13.591832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.003-2.20450.32511250.252730633188
2.2045-2.52350.24341360.209230583194
2.5235-3.17920.26681500.212630853235
3.1792-41.92870.22391280.177532593387
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)
18.3559-0.73761.93193.63293.64394.52090.6511-2.6896-1.10132.1157-0.91251.45430.4074-1.81470.21830.5261-0.15710.03760.68060.04520.357527.5142.086622.7365
22.1915-2.5938-0.23564.48490.19148.2484-0.1196-0.81140.7562.6646-1.4486-1.62290.11150.9191.28910.6077-0.2682-0.04780.7835-0.10180.754333.580349.538621.1122
34.16973.4876-2.6974.0653-2.06534.2578-0.19210.5590.365-0.19710.3266-0.0367-0.1422-0.2618-0.20410.3350.02-0.05690.25360.00010.39346.03165.471716.4167
42.01065.071-2.52132.5777-2.07387.20990.74060.5918-1.20331.20250.23431.60820.3813-1.206-0.81010.54330.02020.07720.50190.17040.972446.468174.879617.4795
53.91245.1926-0.59957.0809-1.59074.08670.3877-0.0721.31892.06020.18011.43640.08430.1989-0.71940.44680.01530.12740.46460.06520.603839.012960.643526.8668
62.49323.88871.47255.26062.74391.6031-0.0295-0.00410.1477-0.05-0.00170.0339-0.0726-0.05650.02380.25020.0109-0.00890.2140.02150.269147.040659.708720.347
78.54423.66785.69043.93451.64394.52110.787-0.4308-1.310.2857-0.1388-0.01850.52-0.3479-0.5420.3511-0.03810.03020.29810.00580.405530.719838.007714.0552
82.52073.1766-0.73633.1743-0.00571.75140.2465-0.06290.15850.70660.00470.0363-0.2053-0.026-0.22740.3242-0.00190.01570.27420.01160.320748.45165.956725.035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 21 )A14 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 26 )A22 - 26
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 36 )A27 - 36
4X-RAY DIFFRACTION4chain 'A' and (resid 37 through 41 )A37 - 41
5X-RAY DIFFRACTION5chain 'A' and (resid 42 through 49 )A42 - 49
6X-RAY DIFFRACTION6chain 'B' and (resid 525 through 578 )B525 - 578
7X-RAY DIFFRACTION7chain 'B' and (resid 579 through 606 )B579 - 606
8X-RAY DIFFRACTION8chain 'B' and (resid 607 through 639 )B607 - 639

+
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