[English] 日本語
Yorodumi
- PDB-5de8: Crystal structure of the complex between human FMRP RGG motif and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5de8
TitleCrystal structure of the complex between human FMRP RGG motif and G-quadruplex RNA, iridium hexammine bound form.
Components
  • Fragile X mental retardation protein 1
  • sc1
KeywordsRNA binding protein/RNA / Fragile X syndrome / RNA structure / RGG box / FMRP / G-quadruplex / RNA binding protein-RNA complex
Function / homology
Function and homology information


positive regulation of intracellular transport of viral material / regulation of translation at presynapse, modulating synaptic transmission / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule ...positive regulation of intracellular transport of viral material / regulation of translation at presynapse, modulating synaptic transmission / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule / animal organ development / negative regulation of voltage-gated calcium channel activity / dendritic filopodium / RNA strand annealing activity / chromocenter / regulation of dendritic spine development / positive regulation of long-term neuronal synaptic plasticity / filopodium tip / regulation of neurotransmitter secretion / regulation of filopodium assembly / negative regulation of synaptic vesicle exocytosis / non-membrane-bounded organelle assembly / regulatory ncRNA-mediated gene silencing / poly(A) binding / positive regulation of proteasomal protein catabolic process / N6-methyladenosine-containing RNA reader activity / siRNA binding / poly(U) RNA binding / glutamate receptor signaling pathway / sequence-specific mRNA binding / miRNA binding / positive regulation of filopodium assembly / intracellular non-membrane-bounded organelle / dynein complex binding / positive regulation of dendritic spine development / dendritic spine neck / regulation of alternative mRNA splicing, via spliceosome / glial cell projection / positive regulation of receptor internalization / chromosome, centromeric region / mRNA transport / negative regulation of cytoplasmic translation / translation regulator activity / mRNA export from nucleus / signaling adaptor activity / Cajal body / stress granule assembly / axon terminus / translation repressor activity / negative regulation of translational initiation / translation initiation factor binding / regulation of mRNA stability / methylated histone binding / RNA splicing / molecular condensate scaffold activity / mRNA 3'-UTR binding / cell projection / positive regulation of translation / mRNA processing / cellular response to virus / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / RNA stem-loop binding / presynapse / ribosome binding / presynaptic membrane / chromosome / nervous system development / growth cone / G-quadruplex RNA binding / postsynapse / microtubule binding / postsynaptic membrane / perikaryon / transmembrane transporter binding / dendritic spine / postsynaptic density / negative regulation of translation / ribonucleoprotein complex / neuron projection / positive regulation of protein phosphorylation / protein heterodimerization activity / axon / DNA repair / mRNA binding / synapse / chromatin binding / dendrite / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain ...Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain / Fragile X-related 1 protein core C terminal / FMRP KH0 domain / Fragile X messenger ribonucleoprotein 1, Tudor domain / Agenet-like domain profile. / Agenet-like domain / Agenet domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
IRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10) / Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1003 Å
AuthorsVasilyev, N. / Polonskaia, A. / Darnell, J.C. / Darnell, R.B. / Patel, D.J. / Serganov, A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R21MH103655 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)TR01 GM104962 United States
Whitehead Institute for Biomedical Research United States
Edward Mallinckrodt, Jr. Foundation United States
New York University United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Crystal structure reveals specific recognition of a G-quadruplex RNA by a beta-turn in the RGG motif of FMRP.
Authors: Vasilyev, N. / Polonskaia, A. / Darnell, J.C. / Darnell, R.B. / Patel, D.J. / Serganov, A.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: sc1
B: Fragile X mental retardation protein 1
C: sc1
D: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,04811
Polymers26,4984
Non-polymers1,5507
Water00
1
A: sc1
B: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1716
Polymers13,2492
Non-polymers9224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-13 kcal/mol
Surface area6090 Å2
MethodPISA
2
C: sc1
D: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8775
Polymers13,2492
Non-polymers6283
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-11 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.650, 130.600, 36.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: RNA chain sc1


Mass: 11459.821 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide Fragile X mental retardation protein 1 / Protein FMR-1


Mass: 1788.939 Da / Num. of mol.: 2 / Mutation: R527A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q06787
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H18IrN6

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate pH 5.6, 0.2 M ammonium acetate, 18% PEG 4000. Incubated with 10 mM iridium hexammine for heavy atom derivation.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.10528 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Oct 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10528 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 9586 / % possible obs: 98.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.7
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 7.45 / Num. unique all: 677 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SAD / Resolution: 3.1003→19.355 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 243 4.56 %
Rwork0.2007 --
obs0.2019 5334 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1003→19.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms170 1518 37 0 1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061898
X-RAY DIFFRACTIONf_angle_d1.2172943
X-RAY DIFFRACTIONf_dihedral_angle_d18.709896
X-RAY DIFFRACTIONf_chiral_restr0.058360
X-RAY DIFFRACTIONf_plane_restr0.006104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.90080.31310.24232437X-RAY DIFFRACTION98
3.9008-19.35580.17131120.1732654X-RAY DIFFRACTION100
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)
10.57570.1602-0.02050.6787-0.04261.78090.0938-0.2115-0.30110.118-0.06190.214-0.186-0.44440.40270.1081-0.0165-0.05910.27230.05650.3933-12.366838.844713.1761
23.9012-0.28651.01163.7887-1.96211.4082-0.07270.80460.2462-1.14240.065-0.72470.24750.170.180.3229-0.14180.1020.37540.040.2877-10.049534.6651.5231
33.37633.1341-1.05513.3019-1.92912.65320.2992-0.22840.70380.6258-0.20521.2212-1.1212-0.4787-0.11610.47990.19290.02930.32690.08170.534-15.913251.761711.0398
42.69320.252-0.36093.2699-0.26010.52010.10190.39730.4536-0.66890.1804-0.0591-0.4505-0.07460.10880.4481-0.02380.01310.09350.05130.2824-9.343449.12596.3682
50.59770.7556-0.43341.0296-0.54440.3238-0.1766-0.0273-0.20710.4211-0.3276-0.04520.0292-0.0091-0.77720.74840.01420.02450.1427-0.18730.2956-10.329574.8369-3.6608
62.2-0.72-1.72324.1429-0.58121.67950.3102-0.0069-0.2832-0.1459-0.51070.5695-0.21370.1009-0.46580.9832-0.0053-0.08010.085-0.01710.2481-15.328987.6409-5.971
75.16080.22211.40710.17770.00810.4029-0.0316-0.82720.43970.8363-0.1730.81840.1786-0.28380.34241.01730.11780.3460.4397-0.02290.6761-22.300386.13163.6512
81.6568-0.62620.52022.32340.37710.74830.0783-0.0364-0.44460.5284-0.23810.8095-0.2547-0.06830.10310.92050.15420.06610.2357-0.120.4621-13.920271.4636-2.0908
92.3079-0.2391.27954.8958-1.20750.94460.3589-0.1255-0.48640.5152-0.12880.4931-0.2505-0.2701-0.00740.80780.02010.0430.2805-0.07640.3762-12.827673.25593.4173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 28 )
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 35 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 18 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 9 )
6X-RAY DIFFRACTION6chain 'C' and (resid 10 through 21 )
7X-RAY DIFFRACTION7chain 'C' and (resid 22 through 26 )
8X-RAY DIFFRACTION8chain 'C' and (resid 27 through 35 )
9X-RAY DIFFRACTION9chain 'D' and (resid 6 through 19 )

+
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