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- PDB-8cmk: Transportin-3 TNPO3 in complex with RSY region of CIRBP -

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Basic information

Entry
Database: PDB / ID: 8cmk
TitleTransportin-3 TNPO3 in complex with RSY region of CIRBP
Components
  • Cold-inducible RNA-binding protein
  • Transportin-3
KeywordsTRANSPORT PROTEIN / Transportin / nuclear import / RNA-binding
Function / homology
Function and homology information


annulate lamellae / positive regulation of mRNA splicing, via spliceosome / mRNA stabilization / nuclear import signal receptor activity / response to UV / translation repressor activity / stress granule assembly / response to cold / positive regulation of translation / mRNA 3'-UTR binding ...annulate lamellae / positive regulation of mRNA splicing, via spliceosome / mRNA stabilization / nuclear import signal receptor activity / response to UV / translation repressor activity / stress granule assembly / response to cold / positive regulation of translation / mRNA 3'-UTR binding / spliceosomal complex / small GTPase binding / protein import into nucleus / cytoplasmic stress granule / nuclear envelope / small ribosomal subunit rRNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RBM3/CIRBP, RNA recognition motif / Transportin-3/Importin-13 second TPR domain / Transportin-3/Importin-13 third TPR domain / Transportin-3/Importin-13 fourth TPR domain / : / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / RNA recognition motif domain, eukaryote / RNA recognition motif ...RBM3/CIRBP, RNA recognition motif / Transportin-3/Importin-13 second TPR domain / Transportin-3/Importin-13 third TPR domain / Transportin-3/Importin-13 fourth TPR domain / : / : / Exportin-1/Importin-beta-like / Exportin 1-like protein / RNA recognition motif domain, eukaryote / RNA recognition motif / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 2-(1H-INDOL-3-YL)ETHANAMINE / Cold-inducible RNA-binding protein / Transportin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.945 Å
AuthorsZhou, Q. / Sagmeister, T. / Pavkov-Keller, T. / Madl, T.
Funding support Austria, 6items
OrganizationGrant numberCountry
Austrian Research Promotion Agency864690 Austria
Austrian Research Promotion Agency870454 Austria
Austrian Science FundP28854 Austria
Austrian Science FundI3792 Austria
Austrian Science FundDOC-130 Austria
Austrian Science FundW1226 Austria
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of phosphorylation-independent nuclear import of CIRBP by TNPO3.
Authors: Zhou, Q. / Sagmeister, T. / Hutten, S. / Bourgeois, B. / Pavkov-Keller, T. / Dormann, D. / Madl, T.
History
DepositionFeb 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transportin-3
B: Transportin-3
C: Cold-inducible RNA-binding protein
D: Cold-inducible RNA-binding protein
E: Cold-inducible RNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,6907
Polymers220,4245
Non-polymers2662
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint7 kcal/mol
Surface area79670 Å2
Unit cell
Length a, b, c (Å)97.526, 101.805, 114.133
Angle α, β, γ (deg.)90.000, 111.128, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transportin-3 / Importin-12 / Imp12 / Transportin-SR / TRN-SR


Mass: 104281.148 Da / Num. of mol.: 2 / Mutation: C511A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO3, IPO12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5L0
#2: Protein/peptide Cold-inducible RNA-binding protein / A18 hnRNP / Glycine-rich RNA-binding protein CIRP


Mass: 3953.921 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIRBP, A18HNRNP, CIRP / Production host: Escherichia coli (E. coli) / References: UniProt: Q14011
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H12N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.5ul Protein (TNPO3) 12mg/ml with 0.2ul Ligand (CIRBP) 4.4mg/ml and 0.1ul seeding stock were mixed with 0.5ul of condition. Condition: 0.1M Sodium HEPES, 0.1M MOPS (acid), 7.5pH, 12.5% v/v ...Details: 0.5ul Protein (TNPO3) 12mg/ml with 0.2ul Ligand (CIRBP) 4.4mg/ml and 0.1ul seeding stock were mixed with 0.5ul of condition. Condition: 0.1M Sodium HEPES, 0.1M MOPS (acid), 7.5pH, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350, 0.05% w/v D-Salicin, 0.05% w/v Esculin hydrate, 0.05% w/v Quinine hemisulfate salt monohydrate, 0.05% w/v Tryptamine, 0.05% w/v Arbutin (in 50% EtOH) Protein and Ligand in 50mM Tris, 150mM NaCl, 2mM TCEP, 0.04% NaN3, pH: 7.5 Buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03322 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.94→48.72 Å / Num. obs: 43555 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.09 / Rrim(I) all: 0.13 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
11.02-48.723.30.0448760.9950.0430.061
2.94-3.063.50.67244580.5090.6290.923

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.945→48.715 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.853 / SU B: 30.297 / SU ML: 0.552 / Cross valid method: FREE R-VALUE / ESU R Free: 0.57
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3166 2105 4.837 %
Rwork0.2464 41418 -
all0.25 --
obs-43523 98.273 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 83.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.559 Å20 Å21.168 Å2
2---1.677 Å20 Å2
3---1.027 Å2
Refinement stepCycle: LAST / Resolution: 2.945→48.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14632 0 19 172 14823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01214939
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614288
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.64220275
X-RAY DIFFRACTIONr_angle_other_deg0.5061.56732872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05151835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.16592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.385102614
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2510686
X-RAY DIFFRACTIONr_chiral_restr0.0740.22360
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023364
X-RAY DIFFRACTIONr_nbd_refined0.2080.23331
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.212452
X-RAY DIFFRACTIONr_nbtor_refined0.1650.27364
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.27857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2276
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4960.272
X-RAY DIFFRACTIONr_nbd_other0.4690.2155
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.6050.23
X-RAY DIFFRACTIONr_mcbond_it4.9088.3987373
X-RAY DIFFRACTIONr_mcbond_other4.9088.3987373
X-RAY DIFFRACTIONr_mcangle_it7.99115.1539197
X-RAY DIFFRACTIONr_mcangle_other7.99115.1549198
X-RAY DIFFRACTIONr_scbond_it4.6298.7317566
X-RAY DIFFRACTIONr_scbond_other4.6278.7317566
X-RAY DIFFRACTIONr_scangle_it7.82515.96311078
X-RAY DIFFRACTIONr_scangle_other7.82515.96411079
X-RAY DIFFRACTIONr_lrange_it14.688102.08862178
X-RAY DIFFRACTIONr_lrange_other14.689102.10862153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.945-3.0210.3741610.33328930.33532310.9010.91694.52180.323
3.021-3.1030.3991470.31230000.31631650.8850.92699.43130.299
3.103-3.1930.3971270.28429440.28830930.8820.94399.28870.267
3.193-3.2910.3461430.27428250.27829990.9150.94898.96630.255
3.291-3.3980.3341420.2526460.25428750.9170.95896.97390.231
3.398-3.5170.3311190.24725010.25128140.9220.96193.10590.23
3.517-3.6490.3421170.24626010.2527290.920.96199.59690.23
3.649-3.7970.3341340.2424600.24525970.9250.96299.88450.225
3.797-3.9650.3051380.22723540.23124980.9370.96699.75980.213
3.965-4.1570.2941160.21522850.21924070.9320.96899.75070.204
4.157-4.380.2751260.2121470.21322870.9450.9799.38780.202
4.38-4.6430.262890.21620700.21821740.9580.96899.310.212
4.643-4.9610.322990.22919020.23420100.9260.96699.55220.227
4.961-5.3540.3880.2518070.25319110.940.96299.16270.248
5.354-5.8580.336940.27816300.28117480.9170.95198.6270.27
5.858-6.5370.353660.2814870.28315930.9330.95597.4890.28
6.537-7.5260.326690.2512870.25414210.930.9695.42580.255
7.526-9.1630.295600.22811320.23111960.9490.96999.66560.238
9.163-12.7350.224480.2139030.2149560.9810.97699.4770.223
12.735-48.7150.435220.3055430.315720.8730.94598.77620.318

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