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- PDB-2c1t: Structure of the Kap60p:Nup2 complex -

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Basic information

Entry
Database: PDB / ID: 2c1t
TitleStructure of the Kap60p:Nup2 complex
Components
  • IMPORTIN ALPHA SUBUNITImportin α
  • NUCLEOPORIN NUP2
KeywordsPROTEIN TRANSPORT/MEMBRANE PROTEIN / ARMADILLO REPEAT / KARYOPHERIN RECYCLING / NLS RELEASE / NUCEAR IMPORT / NUCLEAR PROTEIN / NUCLEOPORIN / PROTEIN TRANSPORT / NUCLEAR TRANSPORT-COMPLEX / NUCLEAR PORE COMPLEX / PHOSPHORYLATION / TRANSLOCATION / PROTEIN TRANSPORT-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


proteasome localization / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / import into nucleus / nuclear pore nuclear basket / importin-alpha family protein binding / NLS-dependent protein nuclear import complex ...proteasome localization / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / import into nucleus / nuclear pore nuclear basket / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / structural constituent of nuclear pore / protein targeting to membrane / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / subtelomeric heterochromatin formation / nuclear pore / protein export from nucleus / small GTPase binding / protein import into nucleus / disordered domain specific binding / nuclear envelope / nuclear membrane / chromosome, telomeric region / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / PH-like domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nucleoporin NUP2 / Importin subunit alpha
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMatsuura, Y. / Stewart, M.
CitationJournal: Embo J. / Year: 2005
Title: Nup50/Npap60 Function in Nuclear Import Complex Disassembly and Importin Recycling
Authors: Matsuura, Y. / Stewart, M.
History
DepositionSep 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMPORTIN ALPHA SUBUNIT
B: IMPORTIN ALPHA SUBUNIT
C: NUCLEOPORIN NUP2
D: NUCLEOPORIN NUP2


Theoretical massNumber of molelcules
Total (without water)112,0074
Polymers112,0074
Non-polymers00
Water2,720151
1
A: IMPORTIN ALPHA SUBUNIT
C: NUCLEOPORIN NUP2


Theoretical massNumber of molelcules
Total (without water)56,0042
Polymers56,0042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IMPORTIN ALPHA SUBUNIT
D: NUCLEOPORIN NUP2


Theoretical massNumber of molelcules
Total (without water)56,0042
Polymers56,0042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.813, 140.076, 63.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110A
210B
111C
211D
112C
212D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A88 - 90
2116B88 - 90
1121A91 - 116
2121B91 - 116
1134A117 - 123
2134B117 - 123
1141A124 - 161
2141B124 - 161
1151A162 - 203
2151B162 - 203
1161A204 - 246
2161B204 - 246
1171A247 - 287
2171B247 - 287
1181A288 - 327
2181B288 - 327
1284A328 - 332
2284B328 - 332
1191A333 - 414
2191B333 - 414
1294A415 - 416
2294B415 - 416
11101A417 - 490
21101B417 - 490
12103A491
22103B491
13101A492 - 510
23101B492 - 510
11115C2 - 3
21115D2 - 3
12111C4 - 14
22111D4 - 14
13115C15 - 17
23115D15 - 17
11126C25 - 29
21126D25 - 29
12126C30 - 42
22126D30 - 42
13126C43 - 45
23126D43 - 45

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein IMPORTIN ALPHA SUBUNIT / Importin α / KAP60P / KARYOPHERIN ALPHA SUBUNIT / SERINE-RICH RNA POLYMERASE I SUPPRESSOR PROTEIN


Mass: 50189.902 Da / Num. of mol.: 2 / Fragment: ARM DOMAIN, RESIDUES 88-541 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02821
#2: Protein NUCLEOPORIN NUP2 / NUP2P / NUCLEAR PORE PROTEIN NUP2 / P95


Mass: 5813.649 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-51
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32499
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIMPORTIN ALPHA SUBUNIT: SPECIFICALLY BINDS TO SUBSTRATES CONTAINING NLS MOTIF AND PROMOTES DOCKING ...IMPORTIN ALPHA SUBUNIT: SPECIFICALLY BINDS TO SUBSTRATES CONTAINING NLS MOTIF AND PROMOTES DOCKING OF IMPORT SUBSTRATES TO THE NUCLEAR ENVELOPE. NUCLEOPORIN NUP2: WORKS AS A COMPONENT OF THE NUCLEAR PORE COMPLEX (NPC). ENGINEERED RESIDUE IN CHAIN A, TYR 397 TO ASP ENGINEERED RESIDUE IN CHAIN B, TYR 397 TO ASP
Sequence detailsRESIDUES 1 TO 87 REMOVED. Y397D INTRODUCED MUTATION ONLY RESIDUES 1 TO 51 PRESENT

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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: 49 %
Crystal growpH: 6.8
Details: EXPERIMENTAL DETALS GIVEN IN ENTRY 1UN0 AND IN MATSUURA ET AL, EMBO J, 22, 5358, 2003., pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 29670 / % possible obs: 97.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EE4

1ee4


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.848 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.673 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1806 5.1 %RANDOM
Rwork0.203 ---
obs0.205 33802 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---1.68 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7122 0 0 151 7273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227226
X-RAY DIFFRACTIONr_bond_other_d0.0010.026742
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.9659810
X-RAY DIFFRACTIONr_angle_other_deg1.023315734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3785915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.21166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027947
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021269
X-RAY DIFFRACTIONr_nbd_refined0.230.21911
X-RAY DIFFRACTIONr_nbd_other0.2310.27933
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.24064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4470.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.06944601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.86267454
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.81152625
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.614102356
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
2A396tight positional0.090.1
4A576tight positional0.080.1
5A605tight positional0.080.1
6A655tight positional0.090.1
7A605tight positional0.090.1
8A623tight positional0.090.1
9A1196tight positional0.10.1
10A1440tight positional0.090.1
11C173tight positional0.090.1
3A120medium positional0.370.4
8A55medium positional0.330.4
9A34medium positional0.440.4
11C29medium positional0.380.4
1A47loose positional0.530.7
10A9loose positional1.350.7
11C41loose positional0.590.7
12C295loose positional0.570.7
2A396tight thermal13.7115
4A576tight thermal12.0615
5A605tight thermal1015
6A655tight thermal9.9415
7A605tight thermal9.115
8A623tight thermal8.3115
9A1196tight thermal6.6715
10A1440tight thermal14.5215
11C173tight thermal5.8315
3A120medium thermal3.9215
8A55medium thermal13.6615
9A34medium thermal6.8415
11C29medium thermal6.5315
1A47loose thermal11.8212
10A9loose thermal7.3112
11C41loose thermal9.1812
12C295loose thermal7.7112
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.366 130
Rwork0.295 2434

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