- PDB-4lir: Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapien... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4lir
Title
Crystal structure of a nucleoporin 35kDa (NUP35) from Homo sapiens at 2.46 A resolution
Components
Nucleoporin NUP53
Keywords
TRANSPORT 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 / 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 ...nuclear pore central transport channel / nuclear pore organization / Nuclear Pore Complex (NPC) Disassembly / 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 / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / SUMOylation of chromatin organization proteins / HCMV Late Events / cellular response to leukemia inhibitory factor / Transcriptional regulation by small RNAs / phospholipid binding / ISG15 antiviral mechanism / HCMV Early Events / nuclear envelope / snRNP Assembly / nuclear membrane / nucleic acid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE 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
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal grow
Temperature: 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
Resolution: 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) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.46-2.52
7.1
0.982
0.8
4738
668
0.982
100
2.52-2.59
7.1
0.784
1
4463
627
0.784
100
2.59-2.67
7.1
0.598
1.3
4405
624
0.598
100
2.67-2.75
7
0.478
1.6
4215
600
0.478
100
2.75-2.84
7
0.399
1.9
4229
600
0.399
100
2.84-2.94
7
0.316
2.4
3982
571
0.316
100
2.94-3.05
7
0.234
3.2
3922
559
0.234
100
3.05-3.18
7.1
0.183
4
3753
532
0.183
100
3.18-3.32
6.9
0.142
5.1
3531
513
0.142
100
3.32-3.48
6.9
0.107
6.6
3466
502
0.107
100
3.48-3.67
6.9
0.085
8.2
3303
480
0.085
100
3.67-3.89
6.9
0.073
9.2
3104
452
0.073
100
3.89-4.16
6.8
0.064
9.9
2904
429
0.064
100
4.16-4.49
6.7
0.055
11.1
2703
401
0.055
100
4.49-4.92
6.6
0.049
12.9
2457
370
0.049
100
4.92-5.5
6.5
0.05
12.7
2270
348
0.05
100
5.5-6.35
6.4
0.066
9.7
1981
311
0.066
100
6.35-7.78
6.2
0.062
9.6
1678
272
0.062
100
7.78-11
5.8
0.043
13.8
1292
221
0.043
99.7
11-28.558
4.7
0.047
11.9
645
137
0.047
93.7
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
SCALA
3.3.20
datascaling
BUSTER-TNT
2.10.0
refinement
MOSFLM
datareduction
SHELXD
phasing
BUSTER
2.10.0
refinement
Refinement
Method 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).
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