- PDB-1xks: The crystal structure of the N-terminal domain of Nup133 reveals ... -
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Basic information
Entry
Database: PDB / ID: 1xks
Title
The crystal structure of the N-terminal domain of Nup133 reveals a beta-propeller fold common to several nucleoporins
Components
Nuclear pore complex protein Nup133
Keywords
PROTEIN TRANSPORT / beta-propeller / helical insertions
Function / homology
Function and homology information
nephron development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore organization / somite development / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) ...nephron development / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore organization / somite development / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / neural tube development / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / neurogenesis / HCMV Late Events / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / kinetochore / HCMV Early Events / Separation of Sister Chromatids / protein import into nucleus / nuclear envelope / snRNP Assembly / nuclear membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / membrane / cytosol Similarity search - Function
Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0781 Å / Relative weight: 1
Reflection
Resolution: 2.35→40.5 Å / Num. obs: 20899 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 71.03 Å2
Reflection shell
Resolution: 2.35→2.39 Å / % possible all: 93.2
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0005
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
CNS
phasing
Refinement
Method to determine structure: SAD Starting model: Model built by SAD data from SeMet derivative Resolution: 2.35→40.46 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.236
2036
9.8 %
RANDOM
Rwork
0.196
-
-
-
obs
0.2
20899
96.5 %
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all
-
20899
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 65.99 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.79 Å2
0 Å2
0 Å2
2-
-
-0.79 Å2
0 Å2
3-
-
-
1.57 Å2
Refinement step
Cycle: LAST / Resolution: 2.35→40.46 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2845
0
0
95
2940
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.025
0.022
2895
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.167
1.952
3934
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.029
5
365
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.669
25.086
116
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.465
15
468
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.311
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.158
0.2
457
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
2147
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.253
0.3
1164
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.33
0.5
1958
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.205
0.5
266
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.257
0.3
29
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.252
0.5
7
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_mcbond_it
2.716
2
1847
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
4.686
3
2966
X-RAY DIFFRACTION
r_scbond_it
2.983
2
1048
X-RAY DIFFRACTION
r_scangle_it
4.539
3
968
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.35→2.42 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.477
135
-
Rwork
0.342
1283
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
3.1279
2.9346
-1.5333
2.7533
-1.4385
0.7516
-0.451
0.103
0.367
0.062
0.3065
0.5468
0.5051
0.1242
0.1445
0.017
-0.0393
-0.087
-0.0882
-0.0172
0.0111
-25.986
23.098
55.174
2
3.4464
2.4002
2.2518
2.2863
1.1007
1.8267
-0.0762
-0.2384
0.4252
0.0763
-0.186
0.4104
0.2269
-0.106
0.2622
0.0873
0.0165
0.0478
-0.0311
-0.106
-0.1134
-22.711
16.764
70.729
3
1.108
-0.3895
0.2866
1.8001
-0.393
1.1978
-0.0183
-0.1821
-0.2115
0.023
0.1372
0.1463
-0.087
0.0005
-0.1189
0.1195
0.1033
0.0099
0.0148
0.0033
-0.2198
-9.882
14.37
74.858
4
0.5347
-0.8219
-0.2568
2.0996
-0.6623
1.4592
-0.2474
-0.0799
0.0945
0.2417
0.2535
0.0763
-0.0063
0.2324
-0.0061
0.1297
0.1981
-0.0316
0.0386
-0.0051
-0.2123
2.346
19.121
71.134
5
0.2648
0.0456
0.4744
2.2138
-1.405
1.8518
0.0471
0.0506
0.2496
-0.1584
-0.1892
0.0793
0.2149
0.3245
0.1421
0.05
0.161
0.0269
0.0717
0.0485
-0.1983
3.971
22.896
59.136
6
1.1922
-1.8652
0.4705
3.149
-1.0855
0.7143
0.1673
0.0929
0.2138
-0.1303
-0.3976
-0.0914
0.1096
0.1175
0.2303
0.0673
0.0688
0.0127
-0.0406
0.0472
-0.0847
-3.861
39.57
49.402
7
2.1151
2.5287
-0.759
3.0233
-0.9075
0.2724
-0.3135
0.1779
0.0549
-0.1263
0.235
0.415
0.0307
0.3097
0.0784
0.0971
0.0327
-0.0524
-0.0275
-0.0634
-0.1278
-16.429
29.1
49.717
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
75 - 87
11 - 23
2
X-RAY DIFFRACTION
1
A
A
450 - 477
386 - 413
3
X-RAY DIFFRACTION
2
A
A
88 - 146
24 - 82
4
X-RAY DIFFRACTION
3
A
A
149 - 201
85 - 137
5
X-RAY DIFFRACTION
4
A
A
206 - 251
142 - 187
6
X-RAY DIFFRACTION
5
A
A
270 - 310
206 - 246
7
X-RAY DIFFRACTION
6
A
A
312 - 397
248 - 333
8
X-RAY DIFFRACTION
7
A
A
404 - 443
340 - 379
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