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- PDB-4fhn: Nup37-Nup120 full-length complex from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 4fhn
TitleNup37-Nup120 full-length complex from Schizosaccharomyces pombe
Components
  • Glutamate dehydrogenase
  • NUCLEOPORIN NUP37
  • Nucleoporin nup120
KeywordsSTRUCTURAL PROTEIN/OXIDOREDUCTASE / PROTEIN COMPLEX / STRUCTURAL PROTEIN / NUCLEAR PORE COMPLEX / MRNA TRANSPORT / PROTEIN TRANSPORT / WD REPEAT / HELICAL DOMAIN / TRANSLOCATION / TRANSPORT / ROSSMANN FOLD / DEHYDROGENASE / NADP BINDING DOMAIN / STRUCTURAL PROTEIN-OXIDOREDUCTASE complex
Function / homology
Function and homology information


Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Transport of Mature mRNA derived from an Intron-Containing Transcript / glutamate dehydrogenase [NAD(P)+] activity / nuclear pore outer ring / structural constituent of nuclear pore ...Transport of the SLBP independent Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Transcriptional regulation by small RNAs / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Transport of Mature mRNA derived from an Intron-Containing Transcript / glutamate dehydrogenase [NAD(P)+] activity / nuclear pore outer ring / structural constituent of nuclear pore / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / amino acid metabolic process / nuclear pore / nuclear periphery / nuclear envelope / nucleotide binding / nucleus / cytosol
Similarity search - Function
Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160 / Nucleoporin Nup37 / Nucleoporin Nup120/160 / Glutamate dehydrogenase / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain ...Nucleoporin NUP120, helical domain / Nucleoporin Nup120/160 / Nucleoporin Nup37 / Nucleoporin Nup120/160 / Glutamate dehydrogenase / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Uncharacterized WD repeat-containing protein C4F10.18 / Nucleoporin nup120 / Glutamate dehydrogenase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.989 Å
AuthorsBilokapic, S. / Schwartz, T.U.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex.
Authors: Bilokapic, S. / Schwartz, T.U.
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Structure summary
Revision 1.2Jan 9, 2013Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Jul 12, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible
Revision 1.5Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / struct_ref_seq_dif
Item: _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 NUP37
B: Nucleoporin nup120
C: NUCLEOPORIN NUP37
D: Nucleoporin nup120
X: Glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)395,2485
Polymers395,2485
Non-polymers00
Water0
1
A: NUCLEOPORIN NUP37
B: Nucleoporin nup120


  • defined by author&software
  • 173 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)173,1922
Polymers173,1922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-13 kcal/mol
Surface area65950 Å2
MethodPISA
2
C: NUCLEOPORIN NUP37
D: Nucleoporin nup120


  • defined by author&software
  • 173 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)173,1922
Polymers173,1922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-15 kcal/mol
Surface area63690 Å2
MethodPISA
3
X: Glutamate dehydrogenase
x 6


  • defined by author&software
  • 293 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)293,1866
Polymers293,1866
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area24980 Å2
ΔGint-35 kcal/mol
Surface area90760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)329.999, 329.999, 350.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 5:83 or resseq 96:216 or resseq 231:283 or resseq 299:389 )A5 - 83
121chain 'A' and (resseq 5:83 or resseq 96:216 or resseq 231:283 or resseq 299:389 )A96 - 216
131chain 'A' and (resseq 5:83 or resseq 96:216 or resseq 231:283 or resseq 299:389 )A231 - 283
141chain 'A' and (resseq 5:83 or resseq 96:216 or resseq 231:283 or resseq 299:389 )A299 - 389
211chain 'C' and (resseq 5:83 or resseq 96:216 or resseq 231:283 or resseq 299:389 )C5 - 83
221chain 'C' and (resseq 5:83 or resseq 96:216 or resseq 231:283 or resseq 299:389 )C96 - 216
231chain 'C' and (resseq 5:83 or resseq 96:216 or resseq 231:283 or resseq 299:389 )C231 - 283
241chain 'C' and (resseq 5:83 or resseq 96:216 or resseq 231:283 or resseq 299:389 )C299 - 389
112chain 'B' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )B1 - 29
122chain 'B' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )B49 - 208
132chain 'B' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )B233 - 397
142chain 'B' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )B404 - 445
152chain 'B' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )B450 - 555
212chain 'D' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )D1 - 29
222chain 'D' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )D49 - 208
232chain 'D' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )D233 - 397
242chain 'D' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )D404 - 445
252chain 'D' and (resseq 1:29 or resseq 49:208 or resseq 233:397 or resseq 404:445 or resseq 450:555 )D450 - 555

NCS ensembles :
ID
1
2
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D). Chain X is a part of another biological unit that is a hexamer. The hexamer is generated from the monomer in the asymmetric unit by the operations: x,y,z and -y,x-y-1,z and -x+y+1,-x,z and -y,-x,-z-1/2 and x,x-y-1,-z-1/2 and -x+y+1,y,-z-1/2. Chain B makes an interactions with chain X. This interaction is structural, not biological.

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Components

#1: Protein NUCLEOPORIN NUP37 / Uncharacterized WD repeat-containing protein C4F10.18 / NUP37


Mass: 43048.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: Nup37, SPAC4F10.18 / Plasmid: modified pETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O36030
#2: Protein Nucleoporin nup120 / Nuclear pore protein nup120


Mass: 130143.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: nup120, SPBC3B9.16c / Plasmid: modified pETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43044
#3: Protein Glutamate dehydrogenase /


Mass: 48864.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs2467, gdhA, Z2793 / Plasmid: modified pETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XDW9

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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: 6.96 Å3/Da / Density % sol: 82.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Bis-Tris/HCl pH 5.75-6.5, 1.75-2.25 M NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 6.984→95.117 Å / Num. obs: 18313 / % possible obs: 99.5 % / Redundancy: 22.4 % / Rsym value: 0.268 / Net I/σ(I): 15.2
Reflection shell

Rmerge(I) obs: 0.026 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
6.98-7.2318.80.33152216762.62395.9
7.23-7.523.80.44081317132.104100
7.5-7.81240.53935716381.458100
7.81-8.1623.90.83771015810.975100
8.16-8.5523.81.23582915080.619100
8.55-9.0223.423373914420.381100
9.02-9.5623.32.93187213690.262100
9.56-10.2222.84.52979213040.166100
10.22-11.0422.55.52730112140.137100
11.04-12.122.46.32499511180.116100
12.1-13.5321.76.92219410210.103100
13.53-15.6221.47.3197169200.099100
15.62-19.1320.38.5160797940.084100
19.13-27.052011.6126666340.059100
27.05-95.11716.211.459053650.04595.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.989→95.117 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.93 / σ(F): 1.34 / Phase error: 36.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3456 939 5.13 %
Rwork0.2854 --
obs0.2884 18313 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 661.573 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 1070.9 Å2 / Biso mean: 672.6255 Å2 / Biso min: 217.25 Å2
Baniso -1Baniso -2Baniso -3
1-11.9001 Å2-0 Å20 Å2
2--11.9001 Å20 Å2
3----23.8002 Å2
Refinement stepCycle: LAST / Resolution: 6.989→95.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24772 0 0 0 24772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625317
X-RAY DIFFRACTIONf_angle_d1.26734368
X-RAY DIFFRACTIONf_chiral_restr0.0763956
X-RAY DIFFRACTIONf_plane_restr0.0064336
X-RAY DIFFRACTIONf_dihedral_angle_d14.9629113
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2638X-RAY DIFFRACTIONPOSITIONAL0.031
12C2638X-RAY DIFFRACTIONPOSITIONAL0.031
21B4013X-RAY DIFFRACTIONPOSITIONAL0.032
22D4013X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6.9892-7.35760.49351400.44722346248697
7.3576-7.81850.38881440.348824222566100
7.8185-8.42190.31321520.245124392591100
8.4219-9.26910.2731320.189424482580100
9.2691-10.60930.27071240.188425052629100
10.6093-13.36270.28141250.202225262651100
13.3627-108.03040.47261220.42022688281099
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)
10.9934-0.4311-0.22370.9894-0.73862.0564-0.98640.61461.31.5264-0.50740.0503-0.1973-1.46070.46643.37411.7280.11642.9624-0.09876.570756.7424-72.688-36.7514
21.06020.65090.72361.06880.43540.3255-0.5549-0.3012-0.03980.7533-0.0154-1.174-0.5257-0.6168-0.5143.8292-0.6331-0.85662.67040.42059.70447.6842-52.7549-39.3912
30.88730.6044-0.56130.6119-0.27760.28490.17050.4190.17390.85251.3799-0.11950.0731-0.2448-0.2115.74550.0404-1.5723.96620.63823.198265.1056-55.3641-27.7706
41.82430.3997-1.12490.9811-0.34490.6748-1.43490.8371-1.2209-0.7975-0.5283-0.317-2.51060.55780.33415.4876-0.5536-1.15734.35760.14044.603775.72895.7386-51.9883
50.77891.1474-1.59191.0070.02592.4633-0.081-0.09450.00470.9549-0.55551.90910.1041-1.3817-0.50614.01471.774-0.83022.3519-0.77974.347656.3302-13.386-46.3882
61.7454-0.90560.81231.7467-0.45011.5411-1.36521.69021.04551.84380.0330.6898-0.0048-0.4964-0.13564.09020.3535-0.7763.6094-0.60823.352548.7488-30.0256-64.9422
71.7059-1.37471.31644.56740.69081.93992.45511.4942.7739-0.4733-0.29080.2459-0.69520.5232-0.83762.60160.7521-0.03593.89410.67645.548474.2249-59.9329-63.2717
80.69480.21661.72583.0721-1.82564.4305-0.1351-0.40941.50211.136-2.6194-0.2796-0.54234.08570.86693.31380.55180.29084.0860.32152.8089101.4262-81.6445-39.6768
90.0994-0.03880.02110.1075-0.15250.1403-0.3598-0.0164-0.27330.2089-0.0019-0.0350.37590.1425-0.3826.54031.452-0.749910.05440.20157.315118.082-55.267310.5324
100.86120.5059-0.6146-0.0147-0.23560.5477-0.9413-1.48681.40490.2885-0.3070.1308-0.1796-0.8089-0.91665.2702-1.543-0.39876.7357-0.49514.4427106.7693-42.537624.744
110.5641-0.3470.04650.01920.1591-0.0292-0.3096-0.3591-0.27630.11440.274-1.8245-0.5394-0.33810.10874.04120.7953-0.83127.8568-0.98765.424596.8639-55.483411.2287
121.32830.22610.7580.2620.21761.29310.5894-1.71440.3320.80370.1132-0.0588-1.4917-1.30560.02854.0141-0.24490.4023.85030.3313.736254.9493-57.507762.4939
130.25520.1513-0.3053-0.0322-0.69380.8224-0.2299-0.6732.2621-0.4101-2.48580.4255-1.39410.3662-0.70655.03060.15190.37364.8196-1.93233.790175.2135-42.986450.9904
140.45680.01010.88731.22680.35940.78040.36040.15740.25060.6658-0.4999-0.4628-1.2388-0.32950.10253.5429-1.08120.47265.0977-0.87074.339399.4863-46.820256.9751
150.61160.1835-0.67110.1992-0.08911.1396-0.6429-0.2265-0.3612-1.1154-0.081-1.03970.3195-0.282-0.376.22881.7535-1.86278.2256-3.44174.2742112.0395-75.227429.6698
160.0191-0.00250.21390.0688-0.25340.1663-0.19520.0968-1.20971.26881.0938-0.7631.9946-0.7522-0.46416.02751.3870.72925.85740.45724.4976109.5496-92.6798-6.0007
171.7037-0.15980.02850.155-0.5312.14331.01051.5247-0.2250.2335-1.25160.80891.9721-0.4213-0.08683.27630.67220.62392.75760.08971.6775143.8535-86.6447-76.7548
181.5589-2.38330.68979.45294.25546.10360.3236-0.54550.8076-2.9555-1.8822-0.3163-1.21840.97530.66322.70750.4251-0.6942.99910.38133.9069129.7192-89.6753-50.6974
193.19092.1289-1.98972.43630.71914.66570.9689-1.20793.50430.6310.13092.28532.2439-1.0655-0.1481.8650.1669-0.49923.35390.59143.569147.4979-79.8791-58.5237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:106)A5 - 106
2X-RAY DIFFRACTION2chain 'A' and (resseq 107:272)A107 - 272
3X-RAY DIFFRACTION3chain 'A' and (resseq 273:389)A273 - 389
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:345)B1 - 345
5X-RAY DIFFRACTION5chain 'B' and (resseq 346:552)B346 - 552
6X-RAY DIFFRACTION6chain 'B' and (resseq 553:838)B553 - 838
7X-RAY DIFFRACTION7chain 'B' and (resseq 839:967)B839 - 967
8X-RAY DIFFRACTION8chain 'B' and (resseq 968:1126)B968 - 1126
9X-RAY DIFFRACTION9chain 'C' and (resseq 5:106)C5 - 106
10X-RAY DIFFRACTION10chain 'C' and (resseq 107:272)C107 - 272
11X-RAY DIFFRACTION11chain 'C' and (resseq 273:389)C273 - 389
12X-RAY DIFFRACTION12chain 'D' and (resseq 1:345)D1 - 345
13X-RAY DIFFRACTION13chain 'D' and (resseq 346:552)D346 - 552
14X-RAY DIFFRACTION14chain 'D' and (resseq 553:838)D553 - 838
15X-RAY DIFFRACTION15chain 'D' and (resseq 839:967)D839 - 967
16X-RAY DIFFRACTION16chain 'D' and (resseq 968:1126)D968 - 1126
17X-RAY DIFFRACTION17chain 'X' and (resseq 6:209)X6 - 209
18X-RAY DIFFRACTION18chain 'X' and (resseq 210:352)X210 - 352
19X-RAY DIFFRACTION19chain 'X' and (resseq 353:447)X353 - 447

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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