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3u1k

Crystal structure of human PNPase

Method: X-RAY DIFFRACTION Dmax: 159.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Polyribonucleotide nucleotidyltransferase 1, mitochondrial

Homo sapiens

UniProt Q8TCS8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 46–669 Fragment：UNP residues 46-669 CIT CITRIC ACID × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；10%(v/v) 2-Propanol, 0.1M Sodium citrate tribasic dihydrate, 26%(v/v) Polyethylene glycol 400 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.13 Å R-free 0.223
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 46–669 Chain C； UniProt 46–669 Chain D； UniProt 46–669 Fragment：UNP residues 46-669 CIT CITRIC ACID × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；10%(v/v) 2-Propanol, 0.1M Sodium citrate tribasic dihydrate, 26%(v/v) Polyethylene glycol 400 , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.13 Å R-free 0.223

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3U1K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5ZF6 Crystal structure of the dimeric human PNPase Deposited 2018-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 46–669（624 aa）
Chain B 46–669（624 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1M citrate buffer (pH 5.0), 10% (v/v) 2-propanol, 26% (v/v) polyethylene glycol 400
Resolution 2.80 Å R-free 0.249
9KJR The cryo-EM structure of human PNPase in the open conformation Deposited 2024-11-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 46–753（708 aa）
Chain B 46–753（708 aa）
Chain C 46–753（708 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
9KJT The cryo-EM structure of human PNPase in the closed conformation Deposited 2024-11-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 46–783（738 aa）
Chain B 46–783（738 aa）
Chain C 46–783（738 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å
9NJB hPNPase RNA pre-catalytic state Deposited 2025-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 3 PDB declaration: tetrameric
Chain A 46–783（738 aa）
Chain B 46–783（738 aa）
Chain C 46–783（738 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.15 Å
9NJC hPNPase bound to PO4 in loop conformation 1 Deposited 2025-02-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 46–783（738 aa）
Chain B 46–783（738 aa）
Chain C 46–783（738 aa）
Not recorded PO4 PHOSPHATE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
9NJD hPNPase bound to PO4 in loop conformation 3 Deposited 2025-02-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 46–783（738 aa）
Chain B 46–783（738 aa）
Chain C 46–783（738 aa）
Not recorded PO4 PHOSPHATE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
9NJE hPNPase bound to PO4 in loop conformation 2 Deposited 2025-02-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 46–783（738 aa）
Chain B 46–783（738 aa）
Chain C 46–783（738 aa）
Not recorded PO4 PHOSPHATE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
9NO0 hPNPase RNA loading state Deposited 2025-03-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 3 PDB declaration: tetrameric
Chain A 46–783（738 aa）
Chain B 46–783（738 aa）
Chain C 46–783（738 aa）
Not recorded PO4 PHOSPHATE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.08 Å
9XYI hPNPase RNA loading state Deposited 2025-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 3 PDB declaration: tetrameric
Chain A 46–783（738 aa）
Chain B 46–783（738 aa）
Chain C 46–783（738 aa）
Not recorded SO4 SULFATE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
9XZF hPNPase RNA loading state with extended RNA in the bottom Deposited 2025-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Homooligomer；Protein × 3 PDB declaration: tetrameric
Chain A 46–783（738 aa）
Chain B 46–783（738 aa）
Chain C 46–783（738 aa）
Not recorded PO4 PHOSPHATE ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PNPT1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–630； UniProt 46–669 Author chain B； PDBConstruct 7–630； UniProt 46–669 Author chain C； PDBConstruct 7–630； UniProt 46–669 Author chain D； PDBConstruct 7–630； UniProt 46–669

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3u1k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3u1k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3u1k
Deposition date deposition_date2011-09-30
Structure title titleCrystal structure of human PNPase
Keywords keywordsRNase PH, KH domain, exoribonuclease, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.15 Å
Radius of gyration Rg (electron density) rg_electron47.25 Å
Forward intensity I(0) i01047520000.00
Molecular weight molecular_weight271020.0 kDa
Excluded volume excluded_volume341010 ų
Envelope volume envelope_volume472680 ų
Hydration-shell volume shell_volume84450 ų
Envelope diameter envelope_diameter161.9 Å
Shell Rg shell_rg50.79 Å
Envelope Rg envelope_rg46.97 Å
Shape Rg shape_rg47.26 Å
Total Rg total_rg47.35 Å
Total atoms total_atoms19033
Residues n_residues2473
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax159.8 Å
Rg (real space) rg_real49.17 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real1.0480e+09
I(0) uncertainty (real space) i0_real_error1.5780e+07
Rg (reciprocal space) rg_reciprocal47.15 Å
I(0) (reciprocal space) i0_reciprocal1047000000.0000
Solution quality estimate total_estimate0.6468
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.3 Å
Skewness Skewness skewness0.555
Kurtosis Kurtosis kurtosis-0.156
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha1.3720
Highest regularization parameter α highest_alpha159100000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.804; Stabil: 0.891; Sysdev: 0.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.350
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id3u1kA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
Domain ID domain_id3u1kA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily400 — Polyribonucleotide nucleotidyltransferase, RNA-binding domain
Domain ID domain_id3u1kA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
Domain ID domain_id3u1kA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
Domain ID domain_id3u1kB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
Domain ID domain_id3u1kB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily400 — Polyribonucleotide nucleotidyltransferase, RNA-binding domain
Domain ID domain_id3u1kB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
Domain ID domain_id3u1kB04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
Domain ID domain_id3u1kC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
Domain ID domain_id3u1kC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily400 — Polyribonucleotide nucleotidyltransferase, RNA-binding domain
Domain ID domain_id3u1kC03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
Domain ID domain_id3u1kC04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
Domain ID domain_id3u1kD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
Domain ID domain_id3u1kD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily400 — Polyribonucleotide nucleotidyltransferase, RNA-binding domain
Domain ID domain_id3u1kD03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily70 — GHMP Kinase, N-terminal domain
Domain ID domain_id3u1kD04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — K Homology domain, type 1
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8. Citations (1)

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9. Files and Curves (10)