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- PDB-5de5: Crystal structure of the complex between human FMRP RGG motif and... -

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Basic information

Entry
Database: PDB / ID: 5de5
TitleCrystal structure of the complex between human FMRP RGG motif and G-quadruplex RNA.
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 / growth cone filopodium / regulation of translation at presynapse, modulating synaptic transmission / regulation of neuronal action potential / modulation by host of viral RNA genome replication / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / animal organ development ...positive regulation of intracellular transport of viral material / growth cone filopodium / regulation of translation at presynapse, modulating synaptic transmission / regulation of neuronal action potential / modulation by host of viral RNA genome replication / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / animal organ development / negative regulation of voltage-gated calcium channel activity / negative regulation of long-term synaptic depression / dendritic filopodium / regulation of dendritic spine development / RNA strand annealing activity / chromocenter / positive regulation of long-term neuronal synaptic plasticity / filopodium tip / regulation of neurotransmitter secretion / regulation of filopodium assembly / negative regulation of synaptic vesicle exocytosis / N6-methyladenosine-containing RNA reader activity / siRNA binding / poly(A) binding / positive regulation of proteasomal protein catabolic process / membraneless organelle assembly / regulatory ncRNA-mediated gene silencing / sequence-specific mRNA binding / miRNA binding / positive regulation of filopodium assembly / poly(U) RNA binding / intracellular membraneless organelle / glutamate receptor signaling pathway / regulation of alternative mRNA splicing, via spliceosome / positive regulation of dendritic spine development / dynein complex binding / positive regulation of receptor internalization / chromosome, centromeric region / glial cell projection / mRNA transport / mRNA export from nucleus / Cajal body / negative regulation of cytoplasmic translation / translation regulator activity / translation repressor activity / translation initiation factor binding / : / negative regulation of translational initiation / signaling adaptor activity / axon terminus / regulation of mRNA stability / stress granule assembly / RNA splicing / positive regulation of translation / mRNA 3'-UTR binding / cell projection / molecular condensate scaffold activity / cellular response to virus / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / RNA stem-loop binding / mRNA processing / cytoplasmic stress granule / nervous system development / presynapse / presynaptic membrane / ribosome binding / chromosome / growth cone / microtubule binding / G-quadruplex RNA binding / dendritic spine / perikaryon / transmembrane transporter binding / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / negative regulation of translation / protein heterodimerization activity / axon / ribonucleoprotein complex / DNA repair / mRNA binding / synapse / dendrite / chromatin binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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
: / RNA / RNA (> 10) / Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0011 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)26,77111
Polymers26,4984
Non-polymers2747
Water724
1
A: sc1
B: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3665
Polymers13,2492
Non-polymers1173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area6470 Å2
MethodPISA
2
C: sc1
D: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4056
Polymers13,2492
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-8 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.060, 130.010, 36.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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.: 7 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na-citrate pH 5.6, 0.2 M ammonium acetate, 18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.1053 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1053 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 10504 / % possible obs: 99.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 12.9
Reflection shellResolution: 3→3.08 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 3.3 / Num. unique all: 783 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.0011→19.218 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 265 4.54 %
Rwork0.1945 --
obs0.1958 5841 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.0011→19.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms164 1518 7 4 1693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031862
X-RAY DIFFRACTIONf_angle_d0.8462861
X-RAY DIFFRACTIONf_dihedral_angle_d15.944893
X-RAY DIFFRACTIONf_chiral_restr0.04360
X-RAY DIFFRACTIONf_plane_restr0.004103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0011-3.77640.28371350.23362706X-RAY DIFFRACTION99
3.7764-19.21830.18351300.17062870X-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)
10.37580.4753-0.03372.06330.3740.45790.2673-0.2110.06410.293-0.3151-0.00720.19460.10560.11930.1981-0.01820.0150.32530.01580.2955-16.812118.585-5.29
24.8454-0.1653-0.13134.119-0.80262.80410.0037-0.3260.2805-0.3583-0.19190.2831-0.3960.09350.14440.1913-0.0588-0.01290.2415-0.05260.2931-17.54332.0175-9.2364
30.53490.8826-0.12071.4597-0.2180.1330.0566-0.136-0.35750.2733-0.1447-0.48520.44140.2640.09850.42350.04120.12150.30350.06660.588-12.858613.9185-7.3421
45.14740.03470.71332.715-1.02323.37880.1610.2033-0.2334-0.1579-0.10890.2318-0.055-0.00210.0160.1779-0.00060.00660.20560.03820.3289-19.59816.3502-11.7177
50.2974-0.47410.27811.1384-0.02220.77470.21270.09550.0656-0.0951-0.3258-0.37850.50580.0516-0.56560.4994-0.03180.090.18090.09050.2384-14.812-16.5534-23.1406
65.2428-0.2345-2.23120.12580.34621.47660.2045-0.8629-0.41521.0579-0.0414-0.52530.71910.3529-0.31730.9653-0.0014-0.37080.3933-0.03030.5291-6.591-19.079-13.495
70.3998-0.1174-0.39440.08190.22630.6540.13590.11880.0894-0.0104-0.1487-0.1524-0.1871-0.0106-0.0560.43930.0366-0.0090.23180.13350.713-15.7432-3.1187-22.5857
82.63930.4698-0.77092.9071-0.98020.47670.0208-0.33620.26940.69860.0162-0.2248-0.1420.0557-0.00630.43120.0511-0.00040.34750.02530.2146-15.8479-7.7343-15.0129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 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 21 )
6X-RAY DIFFRACTION6chain 'C' and (resid 22 through 28 )
7X-RAY DIFFRACTION7chain 'C' and (resid 29 through 35 )
8X-RAY DIFFRACTION8chain 'D' and (resid 6 through 18 )

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