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- PDB-4lir: Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapien... -

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Basic information

Entry
Database: PDB / ID: 4lir
TitleCrystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution
ComponentsNucleoporin NUP53
KeywordsTRANSPORT PROTEIN / NUCLEAR PROTEIN / PF05172 family / Nup53/35/40-type RNA recognition motif / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear pore nuclear basket / 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 ...nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / nuclear pore nuclear basket / 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 / cellular response to leukemia inhibitory factor / HCMV Late Events / Transcriptional regulation by small RNAs / phospholipid binding / ISG15 antiviral mechanism / HCMV Early Events / nuclear envelope / snRNP Assembly / nuclear membrane / nucleic acid binding / intracellular membrane-bounded organelle / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Nucleoporin, NUP53 / RNA-recognition motif (RRM) Nup35-type domain / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / RRM (RNA recognition motif) domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.46 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be published
Title: Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
History
DepositionJul 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoporin NUP53
B: Nucleoporin NUP53


Theoretical massNumber of molelcules
Total (without water)26,2722
Polymers26,2722
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-9 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.590, 70.590, 160.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Nucleoporin NUP53 / 35 kDa nucleoporin / Mitotic phosphoprotein 44 / MP-44 / Nuclear pore complex protein Nup53 / ...35 kDa nucleoporin / Mitotic phosphoprotein 44 / MP-44 / Nuclear pore complex protein Nup53 / Nucleoporin Nup35


Mass: 13136.193 Da / Num. of mol.: 2 / Fragment: UNP residues 151-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC047029, MP44, NUP35, NUP53 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8NFH5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 151-266) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 151-266) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20.0% MPD, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97949,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 12, 2012 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979491
30.979291
ReflectionResolution: 2.46→28.558 Å / Num. all: 9217 / Num. obs: 9217 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rsym value: 0.091 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.46-2.527.10.9820.847386680.982100
2.52-2.597.10.784144636270.784100
2.59-2.677.10.5981.344056240.598100
2.67-2.7570.4781.642156000.478100
2.75-2.8470.3991.942296000.399100
2.84-2.9470.3162.439825710.316100
2.94-3.0570.2343.239225590.234100
3.05-3.187.10.183437535320.183100
3.18-3.326.90.1425.135315130.142100
3.32-3.486.90.1076.634665020.107100
3.48-3.676.90.0858.233034800.085100
3.67-3.896.90.0739.231044520.073100
3.89-4.166.80.0649.929044290.064100
4.16-4.496.70.05511.127034010.055100
4.49-4.926.60.04912.924573700.049100
4.92-5.56.50.0512.722703480.05100
5.5-6.356.40.0669.719813110.066100
6.35-7.786.20.0629.616782720.062100
7.78-115.80.04313.812922210.04399.7
11-28.5584.70.04711.96451370.04793.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.46→28.558 Å / Cor.coef. Fo:Fc: 0.9395 / Cor.coef. Fo:Fc free: 0.9495 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 437 4.78 %RANDOM
Rwork0.1908 ---
obs0.1915 9149 99.78 %-
Displacement parametersBiso max: 177.82 Å2 / Biso mean: 72.734 Å2 / Biso min: 33.51 Å2
Baniso -1Baniso -2Baniso -3
1-5.0807 Å20 Å20 Å2
2--5.0807 Å20 Å2
3----10.1614 Å2
Refine analyzeLuzzati coordinate error obs: 0.385 Å
Refinement stepCycle: LAST / Resolution: 2.46→28.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 0 12 1276
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d602SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes194HARMONIC5
X-RAY DIFFRACTIONt_it1305HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion171SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1482SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1305HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1762HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion2.7
LS refinement shellResolution: 2.46→2.75 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2441 118 4.73 %
Rwork0.197 2375 -
all0.1994 2493 -
obs--99.78 %
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)
15.5242-2.3246-3.11225.01221.50286.1963-0.06520.8815-1.1686-0.0623-0.28150.07870.7169-0.11380.3467-0.25120.01420.027-0.007-0.22960.06929.216523.80180.1026
26.3708-0.71090.49653.44110.08414.7722-0.1225-0.1003-1.06310.4539-0.00330.55460.327-0.86680.1258-0.2589-0.06970.10570.0014-0.020.0627-7.732528.814613.1949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|171 - 250 }A171 - 250
2X-RAY DIFFRACTION2{ B|169 - 252 }B169 - 252

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