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- PDB-2qnd: Crystal Structure of the KH1-KH2 domains from human Fragile X Men... -

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Basic information

Entry
Database: PDB / ID: 2qnd
TitleCrystal Structure of the KH1-KH2 domains from human Fragile X Mental Retardation Protein
ComponentsFMR1 protein
KeywordsRNA BINDING PROTEIN / KH domain / eukaryotic KH domains / tandem KH domains / type I KH domains / Fragile X Mental Retardation Protein / FMRP
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 / poly(G) binding / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule ...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 / poly(G) binding / negative regulation of miRNA-mediated gene silencing / neuronal ribonucleoprotein granule / regulation of neuronal action potential / negative regulation of long-term synaptic depression / intracellular membraneless organelle / histone H3 reader activity / animal organ development / 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 / negative regulation of synaptic vesicle exocytosis / N6-methyladenosine-containing RNA reader activity / poly(A) binding / membraneless organelle assembly / siRNA binding / growth cone filopodium / sequence-specific mRNA binding / 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 / mRNA 3'-UTR binding / molecular condensate scaffold activity / cellular response to virus / RNA stem-loop binding / mRNA 5'-UTR binding / mRNA processing / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / nervous system development / chromosome / presynapse / growth cone / ribosome binding / presynaptic membrane / G-quadruplex RNA binding / microtubule binding / dendritic spine / perikaryon / transmembrane transporter binding / postsynaptic membrane / postsynapse / postsynaptic density / negative regulation of translation / neuron projection / protein heterodimerization activity / ribonucleoprotein complex / axon / DNA repair / mRNA binding / chromatin binding / nucleolus / synapse / dendrite / 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 / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Fragile X messenger ribonucleoprotein 1 / Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsValverde, R. / Regan, L.
CitationJournal: Structure / Year: 2007
Title: Fragile X mental retardation syndrome: structure of the KH1-KH2 domains of fragile X mental retardation protein.
Authors: Valverde, R. / Pozdnyakova, I. / Kajander, T. / Venkatraman, J. / Regan, L.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Residues 331-375 have been deleted in construct; numbering pertains to full length protein. In PDB ...Residues 331-375 have been deleted in construct; numbering pertains to full length protein. In PDB file residue numbered consequetively 1 through 144. residue1=residue216 in full length protein.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMR1 protein
B: FMR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3283
Polymers32,3042
Non-polymers241
Water2,396133
1
A: FMR1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1762
Polymers16,1521
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FMR1 protein


Theoretical massNumber of molelcules
Total (without water)16,1521
Polymers16,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.00, 70.70, 68.16
Angle α, β, γ (deg.)90.00, 107.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FMR1 protein


Mass: 16152.055 Da / Num. of mol.: 2
Fragment: KH1-KH2 domain of hFMRP (residues:216-330, 376-404)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMR1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5PQZ6, UniProt: Q06787*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM Tris-HCl, pH 8.0, 300mM NaCl, 5mM reduced L-Glutathione, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9788, 0.9793, 0.9184
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2005
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97931
30.91841
ReflectionResolution: 1.9→50 Å / Num. obs: 24901 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 4.8 / % possible all: 83.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→24.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.686 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28706 1266 5.2 %RANDOM
Rwork0.22692 ---
obs0.23003 23260 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.603 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å20.78 Å2
2---1.78 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 1 133 2367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222267
X-RAY DIFFRACTIONr_bond_other_d0.0010.021523
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9563062
X-RAY DIFFRACTIONr_angle_other_deg0.89933732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86325.221113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56515408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6261513
X-RAY DIFFRACTIONr_chiral_restr0.080.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022537
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
X-RAY DIFFRACTIONr_nbd_refined0.2190.2473
X-RAY DIFFRACTIONr_nbd_other0.1910.21582
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21125
X-RAY DIFFRACTIONr_nbtor_other0.0860.21249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2126
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0710.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.27
X-RAY DIFFRACTIONr_mcbond_it2.44841701
X-RAY DIFFRACTIONr_mcbond_other0.6114580
X-RAY DIFFRACTIONr_mcangle_it3.19962276
X-RAY DIFFRACTIONr_scbond_it1.5654932
X-RAY DIFFRACTIONr_scangle_it1.6353786
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 66 -
Rwork0.426 1386 -
obs--100 %
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)
11.7673-0.3361-1.24454.49691.85224.0163-0.18250.1906-0.1292-0.19280.03460.19030.4891-0.32890.14780.1056-0.02960.0639-0.12310.0106-0.220641.39132.30114.216
21.66620.8064-1.63937.1258-0.64853.27140.11060.01580.22740.40520.0430.4373-0.1469-0.2341-0.1536-0.09390.03670.0652-0.09990.0133-0.222539.41746.52427.282
31.0128-0.0422-0.44242.0137-0.96213.0924-0.047-0.0628-0.01050.00180.0442-0.1055-0.0622-0.02450.00280.3008-0.03660.1663-0.152-0.0312-0.149149.29168.0746.874
41.24081.15490.311210.78790.6493.29520.0118-0.184-0.19680.35610.2536-0.9987-0.37380.3148-0.2653-0.03850.05340.0886-0.0731-0.0272-0.121350.07859.6425.438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 864 - 86
2X-RAY DIFFRACTION2AA87 - 14487 - 144
3X-RAY DIFFRACTION3BB2 - 822 - 82
4X-RAY DIFFRACTION4BB83 - 14483 - 144

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