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- PDB-4jnv: Crystal structure of the human Nup57CCS3* coiled-coil segment, sp... -

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Basic information

Entry
Database: PDB / ID: 4jnv
TitleCrystal structure of the human Nup57CCS3* coiled-coil segment, space group C2
ComponentsNucleoporin p54
KeywordsTRANSPORT PROTEIN / nucleocytoplasmic transport
Function / homology
Function and homology information


protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways ...protein localization to nuclear inner membrane / nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / SUMOylation of chromatin organization proteins / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / nuclear envelope / snRNP Assembly / nuclear membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.85 Å
AuthorsStuwe, T. / Bley, C.J. / Mayo, D.J. / Hoelz, A.
CitationJournal: Science / Year: 2015
Title: Architecture of the fungal nuclear pore inner ring complex.
Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / ...Authors: Stuwe, T. / Bley, C.J. / Thierbach, K. / Petrovic, S. / Schilbach, S. / Mayo, D.J. / Perriches, T. / Rundlet, E.J. / Jeon, Y.E. / Collins, L.N. / Huber, F.M. / Lin, D.H. / Paduch, M. / Koide, A. / Lu, V. / Fischer, J. / Hurt, E. / Koide, S. / Kossiakoff, A.A. / Hoelz, A.
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Structure summary
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin p54
B: Nucleoporin p54
C: Nucleoporin p54
D: Nucleoporin p54


Theoretical massNumber of molelcules
Total (without water)19,1774
Polymers19,1774
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-58 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.506, 36.623, 63.179
Angle α, β, γ (deg.)90.000, 104.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-510-

HOH

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Components

#1: Protein/peptide
Nucleoporin p54 / Nup54 / 54 kDa nucleoporin


Mass: 4794.343 Da / Num. of mol.: 4 / Fragment: UNP residues 453-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP54 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3B4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1 M sodium acetate, pH 5.3, 1.9 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 13158 / Biso Wilson estimate: 31.69 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.85→19.814 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7725 / SU ML: 0.24 / σ(F): 1.36 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2769 2508 9.93 %
Rwork0.237 --
obs0.241 13157 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.9 Å2 / Biso mean: 48.9279 Å2 / Biso min: 4.09 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 0 22 1086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091092
X-RAY DIFFRACTIONf_angle_d0.9241458
X-RAY DIFFRACTIONf_chiral_restr0.054168
X-RAY DIFFRACTIONf_plane_restr0.004184
X-RAY DIFFRACTIONf_dihedral_angle_d19.243438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.88540.32481260.30351176130289
1.8854-1.92380.32891460.2971284143096
1.9238-1.96560.25331380.25391258139697
1.9656-2.01130.28571350.26071250138597
2.0113-2.06150.2711380.23151210134894
2.0615-2.11720.32011410.23311288142998
2.1172-2.17940.27731410.2211300144198
2.1794-2.24970.30221410.21621297143899
2.2497-2.330.28121420.22431284142698
2.33-2.42310.27091400.22031257139797
2.4231-2.53320.27151380.23281236137496
2.5332-2.66640.27731430.21981294143798
2.6664-2.8330.25491500.22481303145399
2.833-3.05110.28741360.23611283141998
3.0511-3.35680.27611370.23811232136995
3.3568-3.83940.28291400.25171272141299
3.8394-4.82570.24151390.21221265140496
4.8257-19.81540.29811370.26141269140696
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)
10.48231.0049-0.36822.5619-0.93621.5746-0.00650.02140.0245-0.1-0.0126-0.3194-0.04760.11430.01210.1953-0.0251-0.0242-0.0176-0.00420.320612.040114.683629.3605
21.6858-0.06910.82941.33860.76392.11810.19490.4002-0.3585-0.0948-0.13960.41570.1926-0.24080.17370.31050.1167-0.12730.2923-0.19210.3931-9.56615.227719.8884
32.9972.66613.34994.1333.52943.91770.0927-0.58070.07290.1323-0.34550.4510.0134-0.75260.20130.1924-0.152-0.15270.626-0.0750.2588-26.672510.78612.1056
43.50090.8541.00181.35350.37731.8245-0.03150.21130.1153-0.0450.12410.26110.0434-0.3937-0.00740.0413-0.0176-0.02080.11210.03410.0637-12.429315.136722.0793
52.0411-1.1811.86942.37490.2043.2737-0.069-0.05270.20420.1548-0.0054-0.0454-0.076-0.11550.07170.1874-0.01720.01180.1356-0.02150.20834.49618.525531.3342
60.6984-0.18640.32562.823-2.85553.8836-0.0294-0.06420.05350.25520.0090.009-0.1433-0.01660.01080.08090.01740.0501-0.1732-0.11090.21559.09887.032133.2677
74.5666-0.2223.92631.3443-0.0763.60110.0050.73230.0442-0.13620.49360.0040.0127-0.1930.11850.3626-0.2461-0.08360.76130.06950.0337-6.416717.320213.8384
85.99840.10134.74560.22790.06363.76430.00230.6799-0.0029-0.17970.0602-0.1917-0.08410.0661-0.00310.40670.27640.04160.7358-0.07510.2706-5.12846.882110.9616
91.7526-0.5032.53516.12090.90774.11950.00970.0780.1311-0.36150.0081-0.2913-0.50060.08670.00150.19810.04580.07850.0106-0.03360.350112.80244.579830.4782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 451 through 455 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 456 through 481 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 457 through 466 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 467 through 481 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 482 through 490 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 451 through 455 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 456 through 482 )C0
8X-RAY DIFFRACTION8chain 'D' and (resid 460 through 485 )D0
9X-RAY DIFFRACTION9chain 'D' and (resid 486 through 490 )D0

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