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- PDB-3w5k: Crystal structure of Snail1 and importin beta complex -

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Basic information

Entry
Database: PDB / ID: 3w5k
TitleCrystal structure of Snail1 and importin beta complex
Components
  • Importin subunit beta-1
  • Zinc finger protein SNAI1
KeywordsNUCLEAR PROTEIN/METAL BINDING PROTEIN / Importin Beta / nuclear transport factor Snail1 / transcription repressor / NUCLEAR PROTEIN-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / epithelial cell migration / endoplasmic reticulum tubular network ...negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / epithelial cell migration / endoplasmic reticulum tubular network / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / establishment of mitotic spindle localization / astral microtubule organization / Epithelial-Mesenchymal Transition (EMT) during gastrulation / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / aortic valve morphogenesis / regulation of bicellular tight junction assembly / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / nuclear localization sequence binding / mitotic metaphase chromosome alignment / hair follicle morphogenesis / NLS-bearing protein import into nucleus / roof of mouth development / E-box binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / mesoderm formation / mitotic spindle assembly / epithelial to mesenchymal transition / canonical Wnt signaling pathway / pericentric heterochromatin / nuclear pore / positive regulation of epithelial to mesenchymal transition / heterochromatin organization / Notch signaling pathway / Assembly of the ORC complex at the origin of replication / Regulation of PTEN gene transcription / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / ISG15 antiviral mechanism / fibrillar center / small GTPase binding / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cytoplasmic stress granule / osteoblast differentiation / specific granule lumen / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / nuclear envelope / nuclear membrane / ficolin-1-rich granule lumen / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / intracellular membrane-bounded organelle / Neutrophil degranulation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
C2H2-type zinc finger / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeat ...C2H2-type zinc finger / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Zinc finger protein SNAI1 / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsChoi, S. / Yamashita, E. / Yasuhara, N. / Song, J. / Son, S.Y. / Won, Y.H. / Shin, Y.S. / Sekimoto, T. / Park, I.Y. / Yoneda, Y. / Lee, S.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural basis for the selective nuclear import of the C2H2 zinc-finger protein Snail by importin beta.
Authors: Choi, S. / Yamashita, E. / Yasuhara, N. / Song, J. / Son, S.Y. / Won, Y.H. / Hong, H.R. / Shin, Y.S. / Sekimoto, T. / Park, I.Y. / Yoneda, Y. / Lee, S.J.
History
DepositionJan 30, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Mar 20, 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 / 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_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_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_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit beta-1
B: Zinc finger protein SNAI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6426
Polymers126,3802
Non-polymers2624
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-10 kcal/mol
Surface area42590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.210, 77.528, 72.019
Angle α, β, γ (deg.)90.00, 100.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Importin subunit beta-1 / Importin-90 / Karyopherin subunit beta-1 / Nuclear factor p97 / Pore targeting complex 97 kDa subunit / PTAC97


Mass: 97257.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNB1, NTF97 / Plasmid: pGEX4T-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q14974
#2: Protein Zinc finger protein SNAI1 / Protein snail homolog 1 / Protein sna


Mass: 29122.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAI1, SNAH / Plasmid: pGEX4T-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: O95863
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.29 %

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
2901
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONSPring-8 BL44XU1
SYNCHROTRONPAL/PLS 6C12
Detector
TypeIDDetector
ADSC QUANTUM 2101CCD
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→40.331 Å / Num. obs: 41574 / % possible obs: 99.2 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→40 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 1901 5.09 %
Rwork0.2148 --
all0.2173 41574 -
obs0.2173 37359 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7524 0 4 60 7588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0227691
X-RAY DIFFRACTIONf_angle_d1.21810435
X-RAY DIFFRACTIONf_dihedral_angle_d15.2672860
X-RAY DIFFRACTIONf_chiral_restr0.0611197
X-RAY DIFFRACTIONf_plane_restr0.0051360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.66510.30441270.26822604100
2.6651-2.73710.32861630.26592547100
2.7371-2.81760.35491360.26542542100
2.8176-2.90850.3051200.25542591100
2.9085-3.01250.33031450.24532587100
3.0125-3.1330.3021410.23562569100
3.133-3.27560.2731270.23622601100
3.2756-3.44820.28831360.22772565100
3.4482-3.66410.24171550.2032568100
3.6641-3.94670.21261450.19372565100
3.9467-4.34350.22021370.18062594100
4.3435-4.9710.26891380.1901259599
4.971-6.25920.27531300.2299261199
6.2592-40.33570.26061010.2195191972
Refinement TLS params.Method: refined / Origin x: 35.1804 Å / Origin y: -14.3142 Å / Origin z: -17.6476 Å
111213212223313233
T0.3999 Å2-0.0134 Å20.0328 Å2-0.4649 Å2-0.0302 Å2--0.4395 Å2
L0.6207 °20.4449 °20.3859 °2-0.5615 °20.1394 °2--0.7091 °2
S0.0406 Å °0.1059 Å °0.1812 Å °0.0355 Å °-0.0756 Å °0.0804 Å °-0.051 Å °-0.3006 Å °0.025 Å °
Refinement TLS groupSelection details: ALL

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