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- PDB-3lcn: Nab2:Gfd1 complex -

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Basic information

Entry
Database: PDB / ID: 3lcn
TitleNab2:Gfd1 complex
Components
  • Nuclear polyadenylated RNA-binding protein NAB2
  • mRNA transport factor GFD1
KeywordsNUCLEAR PROTEIN / nuclear mRNA export / Metal-binding / Nucleus / RNA-binding / Zinc-finger / Membrane / mRNA transport / Nuclear pore complex / Phosphoprotein / Protein transport / Translocation / Transport
Function / homology
Function and homology information


spliceosome-depend formation of circular RNA / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 7S RNA binding / poly(A) binding / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / regulation of mRNA stability ...spliceosome-depend formation of circular RNA / ribonuclease P RNA binding / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 7S RNA binding / poly(A) binding / positive regulation of transcription by RNA polymerase III / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / regulation of mRNA stability / protein transport / 5S rRNA binding / nuclear membrane / tRNA binding / mRNA binding / protein-containing complex binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
mRNA transport factor GFD1 / GFD1 mRNA transport factor / Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain / Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 ...mRNA transport factor GFD1 / GFD1 mRNA transport factor / Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain / Nuclear abundant poly(A) RNA-binding protein Nab2, N-terminal / Nuclear polyadenylated RNA-binding 2 protein, CCCH zinc finger 1 / Nab2/ZC3H14, N-terminal domain superfamily / : / : / Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) / Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1 / RNA-binding, Nab2-type zinc finger / Nab2-type CCCH zinc finger 4 / Nuclear polyadenylated RNA-binding protein Nab2/ZC3H14 / RNA-binding, Nab2-type zinc finger / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear polyadenylated RNA-binding protein NAB2 / mRNA transport factor GFD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStewart, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis for the function of the Saccharomyces cerevisiae Gfd1 protein in mRNA nuclear export.
Authors: Zheng, C. / Fasken, M.B. / Marshall, N.J. / Brockmann, C. / Rubinson, M.E. / Wente, S.R. / Corbett, A.H. / Stewart, M.
History
DepositionJan 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: Nuclear polyadenylated RNA-binding protein NAB2
B: Nuclear polyadenylated RNA-binding protein NAB2
C: mRNA transport factor GFD1
D: mRNA transport factor GFD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2067
Polymers30,0104
Non-polymers1963
Water1,60389
1
A: Nuclear polyadenylated RNA-binding protein NAB2
C: mRNA transport factor GFD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1364
Polymers15,0052
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-41 kcal/mol
Surface area7620 Å2
MethodPISA
2
B: Nuclear polyadenylated RNA-binding protein NAB2
D: mRNA transport factor GFD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0703
Polymers15,0052
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-33 kcal/mol
Surface area7390 Å2
MethodPISA
3
A: Nuclear polyadenylated RNA-binding protein NAB2
B: Nuclear polyadenylated RNA-binding protein NAB2
C: mRNA transport factor GFD1
D: mRNA transport factor GFD1
hetero molecules

A: Nuclear polyadenylated RNA-binding protein NAB2
B: Nuclear polyadenylated RNA-binding protein NAB2
C: mRNA transport factor GFD1
D: mRNA transport factor GFD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,41314
Polymers60,0208
Non-polymers3926
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area8900 Å2
ΔGint-232 kcal/mol
Surface area26450 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-104 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.833, 121.762, 37.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-77-

HOH

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Components

#1: Protein Nuclear polyadenylated RNA-binding protein NAB2


Mass: 11461.874 Da / Num. of mol.: 2 / Fragment: sequence database residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NAB2, YGL122C / Plasmid: pET20a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P32505
#2: Protein/peptide mRNA transport factor GFD1 / Good for full DBP5 activity protein 1


Mass: 3543.208 Da / Num. of mol.: 2 / Fragment: sequence database residues 123-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GFD1, YM9920.09, YMR255W / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q04839
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 150 mM Zn acetate, 12% PEG400, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9879 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2008 / Details: Si (111)
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 17741 / Num. obs: 17741 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4.9 / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2V75

2v75


Resolution: 2→19.073 Å / SU ML: 0.2 / Isotropic thermal model: isotropic / σ(F): 1.37 / Phase error: 19.7 / Stereochemistry target values: ML / Details: see publication for full details
RfactorNum. reflection% reflection
Rfree0.2263 855 4.83 %
Rwork0.1871 --
obs0.1891 17704 98.86 %
all-17704 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.552 Å2 / ksol: 0.438 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0915 Å2-0 Å20 Å2
2---3.0518 Å20 Å2
3---3.1434 Å2
Refinement stepCycle: LAST / Resolution: 2→19.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 3 89 1977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071902
X-RAY DIFFRACTIONf_angle_d0.8032553
X-RAY DIFFRACTIONf_dihedral_angle_d17.072713
X-RAY DIFFRACTIONf_chiral_restr0.048309
X-RAY DIFFRACTIONf_plane_restr0.003322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12520.23291340.20322760X-RAY DIFFRACTION99
2.1252-2.2890.23971270.18542782X-RAY DIFFRACTION99
2.289-2.51890.2071600.17822775X-RAY DIFFRACTION99
2.5189-2.88230.21411340.17422824X-RAY DIFFRACTION100
2.8823-3.62730.2231530.18132846X-RAY DIFFRACTION100
3.6273-19.07370.23281470.19212862X-RAY DIFFRACTION95
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)
16.66791.2367-1.9613.9074-4.46045.45660.55970.52631.38080.8630.00640.6052-0.3242-0.6875-0.6480.39710.03990.0580.29260.00810.381828.843730.47397.4776
25.8993.28045.87515.07553.21235.88440.19641.375-0.3305-0.64530.50130.27090.73460.9074-0.67080.4827-0.0088-0.09750.4744-0.11090.305922.486117.8234-1.2377
36.0798-1.52160.20215.62574.69144.27351.0781.3498-1.2123-0.7226-0.10550.1424-0.3858-2.0612-0.49140.4387-0.0616-0.24130.8861-0.01880.478216.004922.49352.3263
43.4129-0.1167-2.72812.91762.89924.968-0.13910.2047-0.1396-0.5625-0.2639-0.3723-0.3549-0.23230.28780.30550.0485-0.0160.35590.0270.292818.71625.24279.5928
54.1492-0.19321.34460.11370.16231.20770.0466-0.0944-0.24450.31110.00440.00620.17980.0257-0.05660.28170.03830.02440.28520.01640.279626.272819.80316.1914
66.16575.304-6.7268.5942-4.32768.18940.38810.90671.19410.50740.57492.7219-0.2676-1.3408-0.81960.30110.04980.10750.42550.11810.691817.812614.465311.9141
73.8578-1.34641.69743.90342.73814.04530.19070.4122-0.6080.38830.15960.20290.67740.2015-0.32620.3531-0.0238-0.05620.2766-0.03160.354827.541313.98637.5314
82.00541.2351-1.44047.2958-3.72773.2684-0.0131-1.311-0.01620.86690.1539-0.6045-0.62970.6868-0.26960.3548-0.09540.0160.4134-0.01940.328139.164928.12699.5365
98.15214.51313.44928.88512.52851.5291-0.77961.86250.3582-1.82390.6357-0.0025-0.76061.20770.02360.4947-0.09120.08030.43390.06160.230936.008527.8579-1.0431
101.59420.33351.85041.3721-0.1592.43450.0779-0.1469-0.3450.7425-0.7982-0.1831-0.4183-0.76310.560.4995-0.12310.03030.6104-0.09930.339333.277619.1527-8.0806
113.49030.4266-0.88422.734-0.35841.21570.90251.14250.6758-0.3234-0.2448-1.08380.00070.1566-0.43310.4065-0.02430.21560.7221-0.17191.198754.078514.757117.2865
125.97515.86050.27738.0807-0.41110.33110.35570.0127-0.68780.961-0.0483-0.4724-0.0361-0.1786-0.2290.38740.0167-0.03870.3666-0.01070.361644.84778.549925.548
132.0017.7936-7.02329.3909-4.8194.95260.7735-0.2058-1.52321.207-1.1421-2.07651.8372-0.02510.84570.993-0.32640.00740.72040.29650.924638.208-2.553428.527
143.6967-3.23895.31775.3819-4.23528.8760.0884-0.0101-0.90920.435-0.2662-0.02420.24581.132-0.09440.38870.058-0.00080.4423-0.04470.548747.28430.703520.7874
150.7567-0.16770.30765.6125-0.48990.50650.07970.29610.0735-0.05010.12340.71290.0693-0.1635-0.04870.3430.03230.00570.3117-0.03540.373240.47417.803411.6262
165.60621.06950.62890.9588-1.70414.5404-0.27950.1309-1.4194-1.19810.5532-0.79271.00680.1843-0.22520.51570.0256-0.00810.2354-0.08230.433536.4981-1.235915.6444
175.29964.5723-0.45753.7625-0.43830.98520.09060.4028-0.11170.49120.24840.15520.014-0.1477-0.27940.3289-0.03170.01330.2536-0.03910.429336.180810.00919.8771
182.9742-0.85441.28110.4133-0.85932.8426-0.0146-0.09010.63570.3213-0.58990.1152-0.25310.13260.60470.4322-0.1485-0.05780.4062-0.050.535348.339822.83920.8518
193.86533.27231.14564.4541.55760.58970.2775-0.50880.41711.0763-0.3169-0.29970.44850.1602-0.090.6197-0.0414-0.08210.4212-0.07360.353245.187316.926331.1312
200.96631.57050.77525.54543.85492.8450.5829-0.53980.16211.7493-0.5326-0.11721.9167-1.7725-0.03710.6906-0.23750.1150.7581-0.05410.38836.94414.525336.3241
216.25225.06346.45887.43682.0939.602-0.1985-0.61880.3612-0.1689-0.09191.08310.2769-1.43240.15410.299-0.02790.04560.5040.00110.604510.137121.93312.2856
223.3087-1.5281-0.73476.90686.42668.1717-0.4171-0.5823-0.1405-0.1317-0.0610.8332-0.2264-1.39470.64410.32920.07730.04470.3735-0.05110.316416.747128.252119.1691
237.84080.1776-0.1387.2175-0.03315.4693-1.0038-0.44630.24310.38120.7998-0.6621-0.99960.0523-0.23780.43540.115-0.00120.4966-0.15510.421423.025534.017225.5695
248.81372.3166-1.21532.9272-4.56557.9274-0.0310.0575-1.1484-0.51860.21210.50263.1080.2155-0.39061.19840.2193-0.13520.4823-0.19350.8445.6366-7.832917.0353
257.3269-5.1942-0.44434.32422.10435.5858-0.18780.8351-1.12460.5572-0.03841.37161.0060.38440.3080.54560.09630.06630.4858-0.19440.735447.7027-3.777410.4391
261.17331.77921.34194.81271.03523.5597-0.5979-0.48270.277-0.4436-0.4392-1.3680.00720.42871.02120.36280.15160.05180.59440.01540.67852.67873.85554.7387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:15)
2X-RAY DIFFRACTION2(chain A and resid 16:24)
3X-RAY DIFFRACTION3(chain A and resid 25:29)
4X-RAY DIFFRACTION4(chain A and resid 30:34)
5X-RAY DIFFRACTION5(chain A and resid 35:50)
6X-RAY DIFFRACTION6(chain A and resid 51:56)
7X-RAY DIFFRACTION7(chain A and resid 57:73)
8X-RAY DIFFRACTION8(chain A and resid 74:81)
9X-RAY DIFFRACTION9(chain A and resid 82:91)
10X-RAY DIFFRACTION10(chain A and resid 92:100)
11X-RAY DIFFRACTION11(chain B and resid 4:8)
12X-RAY DIFFRACTION12(chain B and resid 9:21)
13X-RAY DIFFRACTION13(chain B and resid 22:26)
14X-RAY DIFFRACTION14(chain B and resid 27:34)
15X-RAY DIFFRACTION15(chain B and resid 35:50)
16X-RAY DIFFRACTION16(chain B and resid 51:56)
17X-RAY DIFFRACTION17(chain B and resid 57:77)
18X-RAY DIFFRACTION18(chain B and resid 78:83)
19X-RAY DIFFRACTION19(chain B and resid 84:93)
20X-RAY DIFFRACTION20(chain B and resid 94:101)
21X-RAY DIFFRACTION21(chain C and resid 128:136)
22X-RAY DIFFRACTION22(chain C and resid 137:143)
23X-RAY DIFFRACTION23(chain C and resid 144:149)
24X-RAY DIFFRACTION24(chain D and resid 129:134)
25X-RAY DIFFRACTION25(chain D and resid 135:139)
26X-RAY DIFFRACTION26(chain D and resid 140:148)

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