[English] 日本語
Yorodumi
- PDB-5ew7: Crystal structure of C9ORF72 Antisense CCCCGG repeat RNA associat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ew7
TitleCrystal structure of C9ORF72 Antisense CCCCGG repeat RNA associated with Lou Gehrig's disease and frontotemporal dementia, crystallized with Ba2+
ComponentsRNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)-3')
KeywordsRNA / REPEAT EXPANSION DISORDER / GENETIC DISEASE
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsTomchick, D.R. / Dodd, D.W. / Gagnon, K.T. / Corey, D.R.
CitationJournal: Biochemistry / Year: 2016
Title: Pathogenic C9ORF72 Antisense Repeat RNA Forms a Double Helix with Tandem C:C Mismatches.
Authors: Dodd, D.W. / Tomchick, D.R. / Corey, D.R. / Gagnon, K.T.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)-3')
B: RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,20911
Polymers13,8182
Non-polymers3919
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-52 kcal/mol
Surface area7130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.134, 47.659, 59.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: RNA chain RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*CP*CP*C)-3')


Mass: 6909.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.04 M sodium cacodylate, 50 mM KCl, 0.08 M NaCl, 0.012 M spermine, 0.02 M barium chloride, 10% (v/v) (+/-)-2-methyl-2,4-pentanediol, equilibrated against 35% (v/v) (+/-)-2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91967 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2014 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91967 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 12281 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 19.56 Å2 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.053 / Χ2: 0.893 / Net I/av σ(I): 31.074 / Net I/σ(I): 9.7 / Num. measured all: 70731
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.75-1.785.35880.760.5060.916100
1.78-1.815.66160.7530.4570.8851000.982
1.81-1.855.85850.8240.3180.8721000.7010.771
1.85-1.895.85930.80.2810.9351000.6180.68
1.89-1.935.96140.8710.2230.9611000.4960.545
1.93-1.975.86050.9130.1880.9791000.4150.456
1.97-2.025.95950.960.1360.9851000.3040.334
2.02-2.075.96190.9680.1180.9911000.260.285
2.07-2.145.95950.9780.0910.9651000.2040.224
2.14-2.25.96100.9860.0720.9861000.160.176
2.2-2.285.96160.9880.0630.9651000.140.154
2.28-2.385.96020.9910.0460.8751000.1020.112
2.38-2.485.96120.9940.040.8321000.0880.097
2.48-2.615.96130.9960.030.7831000.0680.074
2.61-2.785.96210.9960.0270.8471000.0610.067
2.78-2.995.86180.9960.0261.0431000.0560.062
2.99-3.295.86230.9980.0231.1881000.0520.057
3.29-3.775.76300.9990.0160.8791000.0370.04
3.77-4.755.564410.0090.49499.80.0210.023
4.75-505.26820.9990.010.45997.70.020.022

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 5EW4

5ew4


Resolution: 1.75→37.196 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1126 10 %random
Rwork0.2346 10138 --
obs0.2369 11264 91.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.89 Å2 / Biso mean: 27.1189 Å2 / Biso min: 5.47 Å2
Refinement stepCycle: final / Resolution: 1.75→37.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 818 9 100 927
Biso mean--34.38 27.94 -
Num. residues----41
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017936
X-RAY DIFFRACTIONf_angle_d0.4191408
X-RAY DIFFRACTIONf_chiral_restr0.022195
X-RAY DIFFRACTIONf_plane_restr0.00239
X-RAY DIFFRACTIONf_dihedral_angle_d5.178462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.83050.3613710.300463971048
1.8305-1.9270.28191310.28951180131187
1.927-2.04780.28831500.27711344149499
2.0478-2.20590.26781520.25513721524100
2.2059-2.42780.24071530.242213751528100
2.4278-2.7790.27141520.254913751527100
2.779-3.50080.26821550.22051399155499
3.5008-37.20460.22911620.20261454161699
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)
17.1396-0.58491.65781.08040.07532.9813-0.2962-0.4950.01450.16280.24490.6796-0.3731-0.3370.02150.2410.01440.04810.2122-0.09190.500916.070435.575461.2026
20.3125-0.52620.51052.8892-2.82852.7860.20290.08370.0691-0.4723-0.0328-0.00610.29260.297-0.14480.16880.0027-0.0090.1353-0.00260.118918.639831.334641.5795
35.32650.7234-1.74422.32020.68722.30150.33320.9735-0.6715-0.9531-0.19040.12070.4797-0.2974-0.11190.4150.054-0.01320.2229-0.07390.186123.657132.129422.2301
41.7449-0.4975-0.78131.90331.54341.41780.02620.045-0.7648-0.110.20490.38670.3857-0.1068-0.20750.3638-0.0373-0.080.16960.00780.37219.002931.196429.7365
51.1628-0.2283-0.39962.6219-0.05731.51930.0624-0.26480.15010.09280.2793-0.4348-0.0830.2074-0.170.1992-0.04510.01010.1421-0.01930.122419.084730.270556.4215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:7 )A3 - 7
2X-RAY DIFFRACTION2( CHAIN A AND RESID 8:17 )A8 - 17
3X-RAY DIFFRACTION3( CHAIN A AND RESID 18:21 )A18 - 21
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:11 )B2 - 11
5X-RAY DIFFRACTION5( CHAIN B AND RESID 12:21 )B12 - 21

+
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