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Basic information

Entry
Database: PDB / ID: 3mmy
TitleStructural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1
Components
  • Nuclear pore complex protein Nup98
  • mRNA export factor
KeywordsNUCLEAR PROTEIN / Nuclear Pore Complex / mRNA export
Function / homology
Function and homology information


transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket ...transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / 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 / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of mRNA splicing, via spliceosome / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / mitotic spindle pole / Vpr-mediated nuclear import of PICs / cellular response to organic cyclic compound / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / mRNA export from nucleus / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / ubiquitin binding / promoter-specific chromatin binding / RHO GTPases Activate Formins / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / fibrillar center / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / microtubule binding / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / cell division / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #2360 / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nucleoporin autopeptidase / NUP C-terminal domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Arc Repressor Mutant, subunit A - #2360 / Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nucleoporin autopeptidase / NUP C-terminal domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Arc Repressor Mutant, subunit A / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96 / mRNA export factor RAE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.65 Å
AuthorsHoelz, A. / Ren, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1.
Authors: Ren, Y. / Seo, H.S. / Blobel, G. / Hoelz, A.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: mRNA export factor
B: Nuclear pore complex protein Nup98
C: mRNA export factor
D: Nuclear pore complex protein Nup98
E: mRNA export factor
F: Nuclear pore complex protein Nup98
G: mRNA export factor
H: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,94212
Polymers189,1618
Non-polymers7814
Water14,376798
1
A: mRNA export factor
B: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4853
Polymers47,2902
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-8 kcal/mol
Surface area18200 Å2
MethodPISA
2
C: mRNA export factor
D: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4853
Polymers47,2902
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-7 kcal/mol
Surface area18090 Å2
MethodPISA
3
E: mRNA export factor
F: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4853
Polymers47,2902
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-8 kcal/mol
Surface area18140 Å2
MethodPISA
4
G: mRNA export factor
H: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4853
Polymers47,2902
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-8 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.396, 79.298, 93.407
Angle α, β, γ (deg.)76.63, 89.96, 89.94
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12A
22C
32E
42G
13B
23D
33F
43H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A30 - 260
2112C30 - 260
3112E30 - 260
4112G30 - 260
1122A270 - 368
2122C270 - 368
3122E270 - 368
4122G270 - 368
1132B1 - 300
2132D1 - 300
3132F1 - 300
4132H1 - 300

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
mRNA export factor / mRNA-associated protein mrnp 41 / Rae1 protein homolog


Mass: 41017.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAE1, MRNP41 / Cell (production host): Sf9 cells / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P78406
#2: Protein
Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98 / Nucleoporin Nup98 / 98 kDa nucleoporin


Mass: 6273.065 Da / Num. of mol.: 4 / Fragment: UNP residues 158-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98, ADAR2 / Cell (production host): Sf9 cells / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P52948
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.14014 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14014 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 188056

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.65→19.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.494 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23742 9058 5 %RANDOM
Rwork0.20612 ---
obs0.20769 170317 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.543 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20.19 Å2-0.07 Å2
2---2.78 Å2-0.83 Å2
3---4.69 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12765 0 48 798 13611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.261.93618054
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18551649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35424.444612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.415152187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7841562
X-RAY DIFFRACTIONr_chiral_restr0.0890.21944
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210178
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.25697
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.29039
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2881
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3432.58340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3083.513275
X-RAY DIFFRACTIONr_scbond_it2.5962.55600
X-RAY DIFFRACTIONr_scangle_it3.7243.54755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A923tight positional0.030.05
12C923tight positional0.030.05
13E923tight positional0.030.05
14G923tight positional0.030.05
21A385tight positional0.020.05
22C385tight positional0.020.05
23E385tight positional0.020.05
24G385tight positional0.020.05
31B200tight positional0.030.05
32D200tight positional0.020.05
33F200tight positional0.020.05
34H200tight positional0.030.05
11A881medium positional0.260.5
12C881medium positional0.280.5
13E881medium positional0.220.5
14G881medium positional0.240.5
21A395medium positional0.30.5
22C395medium positional0.250.5
23E395medium positional0.220.5
24G395medium positional0.220.5
31B198medium positional0.410.5
32D198medium positional0.390.5
33F198medium positional0.370.5
34H198medium positional0.360.5
11A923tight thermal0.110.5
12C923tight thermal0.110.5
13E923tight thermal0.110.5
14G923tight thermal0.110.5
21A385tight thermal0.120.5
22C385tight thermal0.130.5
23E385tight thermal0.130.5
24G385tight thermal0.120.5
31B200tight thermal0.080.5
32D200tight thermal0.080.5
33F200tight thermal0.080.5
34H200tight thermal0.070.5
11A881medium thermal0.732
12C881medium thermal0.712
13E881medium thermal0.662
14G881medium thermal0.682
21A395medium thermal0.762
22C395medium thermal0.672
23E395medium thermal0.752
24G395medium thermal0.742
31B198medium thermal0.552
32D198medium thermal0.532
33F198medium thermal0.572
34H198medium thermal0.592
LS refinement shellResolution: 1.65→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 561 -
Rwork0.37 10274 -
obs--78.62 %

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