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

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Basic information

Entry
Database: PDB / ID: 5dea
TitleCrystal structure of the complex between human FMRP RGG motif and G-quadruplex RNA, cesium 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 mRNA metabolic process / regulation of translation at presynapse, modulating synaptic transmission / dendritic filopodium / negative regulation of voltage-gated calcium channel activity / host-mediated perturbation of viral RNA genome replication / positive regulation of miRNA-mediated gene silencing / negative regulation of synaptic vesicle exocytosis / poly(G) binding / negative regulation of miRNA-mediated gene silencing ...positive regulation of intracellular transport of viral material / regulation of mRNA metabolic process / regulation of translation at presynapse, modulating synaptic transmission / dendritic filopodium / negative regulation of voltage-gated calcium channel activity / host-mediated perturbation of viral RNA genome replication / positive regulation of miRNA-mediated gene silencing / negative regulation of synaptic vesicle exocytosis / poly(G) binding / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / negative regulation of long-term synaptic depression / regulation of neuronal action potential / intracellular membraneless organelle / animal organ development / histone H3 reader activity / RNA strand annealing activity / regulation of dendritic spine development / chromocenter / filopodium tip / positive regulation of long-term neuronal synaptic plasticity / regulation of neurotransmitter secretion / regulation of filopodium assembly / N6-methyladenosine-containing RNA reader activity / poly(A) binding / membraneless organelle assembly / siRNA binding / sequence-specific mRNA binding / growth cone filopodium / regulatory ncRNA-mediated gene silencing / positive regulation of filopodium assembly / positive regulation of proteasomal protein catabolic process / miRNA binding / poly(U) RNA binding / positive regulation of dendritic spine development / regulation of alternative mRNA splicing, via spliceosome / glutamate receptor signaling pathway / dynein complex binding / positive regulation of receptor internalization / chromosome, centromeric region / glial cell projection / mRNA transport / Cajal body / mRNA export from nucleus / cell projection / negative regulation of cytoplasmic translation / regulation of mRNA stability / translation regulator activity / translation repressor activity / negative regulation of translational initiation / signaling adaptor activity / translation initiation factor binding / RNA splicing / excitatory synapse / axon terminus / stress granule assembly / positive regulation of translation / cellular response to virus / mRNA 3'-UTR binding / molecular condensate scaffold activity / RNA stem-loop binding / mRNA 5'-UTR binding / cytoplasmic ribonucleoprotein granule / mRNA processing / cytoplasmic stress granule / nervous system development / presynapse / chromosome / growth cone / ribosome binding / presynaptic membrane / G-quadruplex RNA binding / microtubule binding / dendritic spine / perikaryon / transmembrane transporter binding / postsynaptic membrane / postsynapse / postsynaptic density / neuron projection / negative regulation of translation / protein heterodimerization activity / ribonucleoprotein complex / axon / DNA repair / mRNA binding / chromatin binding / nucleolus / dendrite / synapse / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / 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: 2.7973 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 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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

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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)27,05311
Polymers26,4984
Non-polymers5557
Water1448
1
A: sc1
B: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4605
Polymers13,2492
Non-polymers2113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-50 kcal/mol
Surface area6240 Å2
MethodPISA
2
C: sc1
D: Fragile X mental retardation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5936
Polymers13,2492
Non-polymers3444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-87 kcal/mol
Surface area6020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.570, 129.870, 36.790
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.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cs
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate pH 5.6, 0.1 M ammonium acetate, 0.1 M cesium chloride, 18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.4938 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Dec 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4938 Å / Relative weight: 1
ReflectionResolution: 2.797→20 Å / Num. obs: 12553 / % possible obs: 97.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.3
Reflection shellResolution: 2.797→2.87 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 4.4 / Num. unique all: 639 / % possible all: 69.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DE8

5de8


Resolution: 2.7973→19.867 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 331 4.76 %
Rwork0.2015 --
obs0.2027 6947 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7973→19.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms170 1518 7 8 1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041868
X-RAY DIFFRACTIONf_angle_d1.2872868
X-RAY DIFFRACTIONf_dihedral_angle_d17.871896
X-RAY DIFFRACTIONf_chiral_restr0.066360
X-RAY DIFFRACTIONf_plane_restr0.007104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7973-3.52110.2721620.23523145X-RAY DIFFRACTION95
3.5211-19.86760.19731690.18193471X-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)
10.0104-0.0175-0.02560.04380.0550.07150.00150.0993-0.1135-0.0659-0.0057-0.0543-0.0428-0.1319-0.02050.14260.08930.05630.2185-0.00990.1695-11.32219.2035-13.163
20.0407-0.0588-0.00720.1083-0.02690.0609-0.0071-0.0264-0.0012-0.0197-0.02520.011-0.0473-0.1199-0.1790.12160.13380.02190.33140.03940.091-17.034135.0903-14.8954
30.1065-0.10950.07160.1174-0.07910.0529-0.0398-0.0476-0.00060.03490.0089-0.0651-0.0301-0.0335-0.27750.10450.08610.03180.09690.040.0821-10.068424.9012-7.6315
40.06210.0093-0.0580.0028-0.00880.0540.00560.02570.01340.01160.0166-0.019-0.002-0.01050.05240.04520.0388-0.0330.079-0.03940.1245-8.637616.8478-6.7776
50.0413-0.0110.03290.21610.05220.04620.007-0.0740.01070.209-0.07880.1050.2617-0.0913-0.34780.3007-0.10980.05930.0325-0.03470.1041-13.7557-15.95854.7171
60.02460.01910.02150.01890.03790.11820.00020.01390.0019-0.0508-0.01380.01750.0313-0.0432-0.09090.3627-0.0957-0.09860.17160.05560.1472-22.0603-18.2415-5.1922
70.12220.05880.0030.0338-0.00690.01550.0119-0.017-0.01190.01940.00060.09320.013-0.0150.01990.0956-0.01190.02690.1045-0.06480.4575-12.7098-2.5664.1411
80.01030.0020.00630.1012-0.03360.016-0.0010.01870.0034-0.02210.0325-0.0170.01230.00060.03640.0703-0.062-0.03790.1409-0.00260.1118-12.6254-6.4242-3.4083
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 16 )
3X-RAY DIFFRACTION3chain 'A' and (resid 17 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 5 through 18 )

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