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- PDB-32qt: Human NUP98 APD (SG P21) -

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Basic information

Entry
Database: PDB / ID: 32qt
TitleHuman NUP98 APD (SG P21)
ComponentsNuclear pore complex protein Nup98
KeywordsNUCLEAR PROTEIN / NUP98 / Nucleoporin 98
Function / homology
Function and homology information


telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore outer ring / nuclear pore organization / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear inclusion body ...telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore outer ring / nuclear pore organization / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / positive regulation of mRNA splicing, via spliceosome / Transport of Mature mRNA Derived from an Intronless Transcript / NS1 Mediated Effects on Host Pathways / 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 / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / nuclear localization sequence binding / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / nuclear pore / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / nuclear periphery / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / serine-type peptidase activity / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / molecular condensate scaffold activity / promoter-specific chromatin binding / protein import into nucleus / RHO GTPases Activate Formins / ISG15 antiviral mechanism / HCMV Early Events / Separation of Sister Chromatids / nuclear envelope / nuclear membrane / snRNP Assembly / nuclear body / transcription coactivator activity / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol
Similarity search - Function
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 / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile.
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsKim, Y. / Schallmayer, L. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Human NUP98 APD (SG P21)
Authors: Kim, Y. / Schallmayer, L. / Knapp, S. / Kraemer, A. / Structural Genomics Consortium (SGC)
History
DepositionJul 21, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6968
Polymers17,2621
Non-polymers4347
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint16 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.935, 73.304, 40.815
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nuclear pore complex protein Nup98 / 98 kDa nucleoporin / Nucleoporin Nup98 / Nup98


Mass: 17261.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98, ADAR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52948
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.47→39.753 Å / Num. obs: 16976 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Net I/σ(I): 10.2
Reflection shellResolution: 1.475→1.618 Å / % possible obs: 12.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 1.176 / Num. measured all: 6395 / Num. unique obs: 849 / Rpim(I) all: 0.46 / Rrim(I) all: 1.263 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→39.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.23 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20728 854 5 %RANDOM
Rwork0.16897 ---
obs0.17103 16121 58.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.594 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20.28 Å2
2---0.14 Å20 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.47→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 28 140 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121268
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161197
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.831705
X-RAY DIFFRACTIONr_angle_other_deg0.51.7622756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4535156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.1859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10110205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5691.997621
X-RAY DIFFRACTIONr_mcbond_other3.5541.996621
X-RAY DIFFRACTIONr_mcangle_it5.4583.588778
X-RAY DIFFRACTIONr_mcangle_other5.4593.589779
X-RAY DIFFRACTIONr_scbond_it4.8432.303647
X-RAY DIFFRACTIONr_scbond_other4.8412.309648
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2414.07928
X-RAY DIFFRACTIONr_long_range_B_refined10.81623.951391
X-RAY DIFFRACTIONr_long_range_B_other10.81623.961392
X-RAY DIFFRACTIONr_rigid_bond_restr2.61532465
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.475→1.513 Å
RfactorNum. reflection% reflection
Rfree0.351 3 -
Rwork0.254 49 -
obs--23.5 %

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