[English] 日本語
Yorodumi
- PDB-5tbx: hnRNP A18 RNA Recognition Motif -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tbx
TitlehnRNP A18 RNA Recognition Motif
ComponentsCold-inducible RNA-binding protein
KeywordsRNA BINDING PROTEIN / RNA-binding protein
Function / homology
Function and homology information


mRNA stabilization / positive regulation of mRNA splicing, via spliceosome / stress granule assembly / response to UV / translation repressor activity / response to cold / positive regulation of translation / mRNA 3'-UTR binding / spliceosomal complex / small ribosomal subunit rRNA binding ...mRNA stabilization / positive regulation of mRNA splicing, via spliceosome / stress granule assembly / response to UV / translation repressor activity / response to cold / positive regulation of translation / mRNA 3'-UTR binding / spliceosomal complex / small ribosomal subunit rRNA binding / cytoplasmic stress granule / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
RBM3/CIRBP, RNA recognition motif / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily ...RBM3/CIRBP, RNA recognition motif / RNA recognition motif domain, eukaryote / RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / Cold-inducible RNA-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.767 Å
AuthorsCoburn, K.M. / Melville, Z. / Aligholizadeh, E. / Roth, B.M. / Varney, K.M. / Weber, D.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-58888 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA-107331 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of the human heterogeneous ribonucleoprotein A18 RNA-recognition motif.
Authors: Coburn, K. / Melville, Z. / Aligholizadeh, E. / Roth, B.M. / Varney, K.M. / Carrier, F. / Pozharski, E. / Weber, D.J.
History
DepositionSep 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cold-inducible RNA-binding protein
B: Cold-inducible RNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4604
Polymers20,3422
Non-polymers1182
Water2,180121
1
A: Cold-inducible RNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2893
Polymers10,1711
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cold-inducible RNA-binding protein


Theoretical massNumber of molelcules
Total (without water)10,1711
Polymers10,1711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.473, 56.149, 72.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cold-inducible RNA-binding protein / A18 hnRNP / Glycine-rich RNA-binding protein CIRP


Mass: 10171.226 Da / Num. of mol.: 2 / Fragment: UNP residues 1-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIRBP, A18HNRNP, CIRP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14011
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M sodium acetate trihydrate pH 8.0 in 20% w/v PEG 3350 from the PEG/Ion HT crystallization screen (Hampton Research, HR2-139).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.77→72.43 Å / Num. obs: 17190 / % possible obs: 99.8 % / Redundancy: 8.5 % / Biso Wilson estimate: 22.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.055 / Rrim(I) all: 0.163 / Net I/σ(I): 13.5 / Num. measured all: 146455 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.77-1.87.93.55373449250.5061.2993.7910.796.2
9.01-72.436.60.022111817010.0090.02456.499.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.77 Å44.38 Å
Translation1.77 Å44.38 Å

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.21data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: hnRNP A1

Resolution: 1.767→44.377 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 883 5.22 %
Rwork0.2175 16043 -
obs0.2191 16926 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.78 Å2 / Biso mean: 37.3898 Å2 / Biso min: 13.08 Å2
Refinement stepCycle: final / Resolution: 1.767→44.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 8 121 1481
Biso mean--46 40.7 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151379
X-RAY DIFFRACTIONf_angle_d1.0861829
X-RAY DIFFRACTIONf_chiral_restr0.058193
X-RAY DIFFRACTIONf_plane_restr0.007249
X-RAY DIFFRACTIONf_dihedral_angle_d13.981834
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7672-1.87790.40461300.3782567269796
1.8779-2.02290.34431450.32222559270497
2.0229-2.22640.2841450.227526642809100
2.2264-2.54860.26451370.21827072844100
2.5486-3.21080.26681580.199227122870100
3.2108-44.39050.18911680.182128343002100
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)
16.8587-0.35390.46825.2278-0.64196.52720.03650.29330.25080.00530.1227-0.06370.0828-0.226-0.1010.1404-0.0146-0.03440.1496-0.01670.1736-11.4862-1.348510.451
28.6112-1.5986-2.79423.6077-3.71992.14020.4260.67050.4753-0.0204-0.223-0.0779-0.56950.0342-0.2160.17330.00250.02320.24630.0360.1934-2.32542.304512.4782
35.9629-2.35923.38327.3861.29462.11560.37640.1229-0.4330.2381-0.0371-0.14620.4932-0.0182-0.30590.1416-0.02220.02360.17990.05230.2-3.5403-4.566613.9519
46.2086-2.2498-2.79555.37431.29492.09370.11840.6346-0.6009-0.6831-0.32580.32380.2838-0.38720.19890.2907-0.0182-0.02990.3009-0.02650.1949-12.9174-3.2256-3.3708
53.2662-0.50182.06353.61650.36137.50090.053-0.2713-0.0770.4487-0.0753-0.03290.3107-0.03020.02670.169-0.03730.01160.17150.03910.1724-8.7434-3.891619.462
68.86964.6346-7.41642.02181.87372.08080.02030.16940.57010.26320.03420.1473-0.9648-0.4113-0.01330.242-0.0036-0.01970.25420.00240.292-13.27289.244413.1315
76.47951.75190.76952.1038-0.34538.8502-0.2459-0.2235-0.9785-1.06080.45910.53360.5569-1.2078-0.29510.2733-0.1038-0.02650.3220.05280.3709-17.3812-5.929114.2134
89.9238-2.34872.69476.10440.19275.40550.29180.2918-1.6399-0.3592-0.0112-0.64720.74140.3898-0.30190.28170.0220.01380.2505-0.01180.448314.7759-8.14140.4661
96.23081.02840.15023.06110.56144.45840.1526-0.28770.54580.1986-0.13860.1846-0.2731-0.1880.10820.1697-0.00510.03520.1301-0.03190.23065.08814.143844.9784
108.35321.83262.05277.972.60052.03350.7323-0.1236-0.98730.28780.05020.23090.9784-0.6833-0.86010.1779-0.0512-0.01960.1790.01970.27793.2475-5.515143.2999
116.97150.9976-3.24089.1769-2.12672.1179-0.2231-0.3087-0.32980.370.38970.01320.5363-0.3660.05360.29410.0328-0.04430.262-0.00950.176112.7583-3.003958.3476
123.10150.11041.91473.4252-0.12817.93530.0640.3197-0.1623-0.3196-0.16050.18030.4167-0.31690.03130.17320.005-0.00220.2228-0.05380.17918.7042-3.617135.8375
132.1439-2.6992-3.60122.21688.90192.0694-0.05220.14080.7584-0.71370.16460.0344-1.7698-0.1859-0.3340.5262-0.0328-0.00070.2490.05650.292312.88819.573642.0228
142.3264-2.3380.13397.2129-2.09085.27580.1731-0.0191-0.74651.3526-0.3077-0.5030.9050.3329-0.07990.5893-0.0495-0.10520.4248-0.02790.341615.3941-8.554944.2124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 19 )A4 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 29 )A20 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 38 )A30 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 49 )A39 - 49
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 68 )A50 - 68
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 78 )A69 - 78
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 86 )A79 - 87
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 12 )B1 - 12
9X-RAY DIFFRACTION9chain 'B' and (resid 13 through 30 )B13 - 30
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 38 )B31 - 38
11X-RAY DIFFRACTION11chain 'B' and (resid 39 through 49 )B39 - 49
12X-RAY DIFFRACTION12chain 'B' and (resid 50 through 68 )B50 - 68
13X-RAY DIFFRACTION13chain 'B' and (resid 69 through 78 )B69 - 78
14X-RAY DIFFRACTION14chain 'B' and (resid 79 through 92 )B79 - 92

+
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