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- PDB-6dcl: Crystal structure of UP1 bound to pri-miRNA-18a terminal loop -

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Basic information

Entry
Database: PDB / ID: 6dcl
TitleCrystal structure of UP1 bound to pri-miRNA-18a terminal loop
Components
  • Heterogeneous nuclear ribonucleoprotein A1
  • RNA (5'-R(*AP*GP*UP*AP*GP*AP*UP*UP*AP*GP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / RRM / hnRNP A1 / RNA / Complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / pre-mRNA binding / G-rich strand telomeric DNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / pre-mRNA binding / G-rich strand telomeric DNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of telomere maintenance via telomerase / mRNA transport / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / 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 ...hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / 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
RNA / RNA (> 10) / Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.497 Å
AuthorsKooshapur, H. / Sattler, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 Germany
German Research Foundation (DFG)GRK1721 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1.
Authors: Kooshapur, H. / Choudhury, N.R. / Simon, B. / Muhlbauer, M. / Jussupow, A. / Fernandez, N. / Jones, A.N. / Dallmann, A. / Gabel, F. / Camilloni, C. / Michlewski, G. / Caceres, J.F. / Sattler, M.
History
DepositionMay 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein A1
B: Heterogeneous nuclear ribonucleoprotein A1
C: RNA (5'-R(*AP*GP*UP*AP*GP*AP*UP*UP*AP*GP*C)-3')
D: RNA (5'-R(*AP*GP*UP*AP*GP*AP*UP*UP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0965
Polymers51,0344
Non-polymers621
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-13 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.028, 127.028, 147.064
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11C-110-

HOH

21C-111-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and resid 3 through 10)
21(chain D and resid 3 through 10)
12(chain A and (resid 8 through 22 or resid 24...
22(chain B and (resid 8 through 22 or resid 24...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111UUGG(chain C and resid 3 through 10)CC3 - 103 - 10
211UUGG(chain D and resid 3 through 10)DD3 - 103 - 10
112LYSLYSSERSER(chain A and (resid 8 through 22 or resid 24...AA8 - 2211 - 25
122GLUGLULYSLYS(chain A and (resid 8 through 22 or resid 24...AA24 - 5227 - 55
132SERSERGLNGLN(chain A and (resid 8 through 22 or resid 24...AA54 - 9657 - 99
142PROPROILEILE(chain A and (resid 8 through 22 or resid 24...AA98 - 131101 - 134
152VALVALASPASP(chain A and (resid 8 through 22 or resid 24...AA133 - 139136 - 142
162LYSLYSSERSER(chain A and (resid 8 through 22 or resid 24...AA145 - 182148 - 185
212LYSLYSSERSER(chain B and (resid 8 through 22 or resid 24...BB8 - 2211 - 25
222GLUGLULYSLYS(chain B and (resid 8 through 22 or resid 24...BB24 - 5227 - 55
232SERSERGLNGLN(chain B and (resid 8 through 22 or resid 24...BB54 - 9657 - 99
242PROPROILEILE(chain B and (resid 8 through 22 or resid 24...BB98 - 131101 - 134
252VALVALSERSER(chain B and (resid 8 through 22 or resid 24...BB133 - 182136 - 185

NCS ensembles :
ID
1
2

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein A1 / hnRNP A1 / Helix-destabilizing protein / Single-strand RNA-binding protein / hnRNP core protein A1


Mass: 21656.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1, HNRPA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09651
#2: RNA chain RNA (5'-R(*AP*GP*UP*AP*GP*AP*UP*UP*AP*GP*C)-3')


Mass: 3860.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.497→48.07 Å / Num. obs: 24934 / % possible obs: 99.9 % / Redundancy: 9.8 % / Biso Wilson estimate: 52.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.028 / Rrim(I) all: 0.094 / Net I/σ(I): 19.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.953 / Num. unique obs: 2731 / CC1/2: 0.801 / Rpim(I) all: 0.316 / Rrim(I) all: 1.008 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.9data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.497→48.066 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.44
RfactorNum. reflection% reflection
Rfree0.2281 1259 5.06 %
Rwork0.2019 --
obs0.2032 24892 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 171.22 Å2 / Biso mean: 72.3367 Å2 / Biso min: 24.82 Å2
Refinement stepCycle: final / Resolution: 2.497→48.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 451 4 72 3373
Biso mean--62.35 47.01 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083410
X-RAY DIFFRACTIONf_angle_d1.0724684
X-RAY DIFFRACTIONf_chiral_restr0.06520
X-RAY DIFFRACTIONf_plane_restr0.006532
X-RAY DIFFRACTIONf_dihedral_angle_d13.2941999
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C186X-RAY DIFFRACTION9.971TORSIONAL
12D186X-RAY DIFFRACTION9.971TORSIONAL
21A1605X-RAY DIFFRACTION9.971TORSIONAL
22B1605X-RAY DIFFRACTION9.971TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4972-2.59720.36921260.32222556268299
2.5972-2.71530.34121430.276225602703100
2.7153-2.85850.32581280.262525872715100
2.8585-3.03760.28311250.257525992724100
3.0376-3.2720.26071370.248826032740100
3.272-3.60120.21761460.21426082754100
3.6012-4.12210.20211460.175326242770100
4.1221-5.19240.20091640.157326472811100
5.1924-48.07480.19251440.174928492993100
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)
11.32262.21410.70016.2044-0.38711.940.0073-0.08930.0840.2875-0.16080.164-0.1633-0.00450.13930.25630.17560.0330.4269-0.04150.28942.029518.9667-11.4928
29.15361.3928-5.76257.48291.36017.30340.11531.6870.4507-0.8966-0.00090.8041-0.313-1.0864-0.10260.46980.2568-0.03540.7804-0.00070.4291-4.946424.4001-26.4352
33.48621.8330.84352.9632-1.26165.55130.43291.02080.6848-1.04-0.0423-0.0693-0.6970.1545-0.37670.86890.39870.24950.85630.17920.65762.952738.5269-33.9568
41.481-0.92020.11551.4370.10990.54160.13110.24960.5145-0.4007-0.1302-0.25-0.3694-0.04810.12211.21510.76060.16380.84590.14940.7897-18.344656.1483-29.4791
57.568-1.1236-2.87710.44780.80811.61150.12310.6097-1.227-0.5827-0.46880.28810.0636-0.08190.30160.97670.63860.0790.920.05460.7231-19.73539.078-29.1127
64.9376-2.69071.12877.7438-0.30241.55580.1169-0.1428-0.01760.3156-0.06340.5616-0.217-0.8907-0.04370.54220.35870.09940.89750.02430.4787-22.143433.0126-12.8201
71.9199-2.53630.14143.4004-0.19330.0516-0.5104-0.5226-0.50630.470.19420.9534-0.0283-0.72180.29520.43030.25760.0240.8999-0.11020.5909-14.63116.9556-20.7373
80.1758-0.7279-0.05132.97510.21790.01510.57271.4130.3844-0.535-0.632-0.0003-0.0810.1399-0.00281.22550.79780.12911.41840.20390.6438-14.226243.3204-40.9288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 88 )A8 - 88
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 105 )A89 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 188 )A106 - 188
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 88 )B8 - 88
5X-RAY DIFFRACTION5chain 'B' and (resid 89 through 105 )B89 - 105
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 183 )B106 - 183
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 11 )C1 - 11
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 11 )D1 - 11

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