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3h1c

Crystal structure of Polynucleotide Phosphorylase (PNPase) core bound to RNase E and Tungstate

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Polyribonucleotide nucleotidyltransferase

OrganismNot specified

UniProt P05055

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 3 TUNGSTATE(VI)ION × 5 Consistent with protein count
13 Protein homooligomer Homooligomer Protein 3 TUNGSTATE(VI)ION × 6 Consistent with protein count
5 Protein homooligomer Homooligomer Protein 3 TUNGSTATE(VI)ION × 4 Consistent with protein count
9 Protein homooligomer Homooligomer Protein 3 TUNGSTATE(VI)ION × 6 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1sro

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
3h1c 3h1c 3h1c 3h1c 7ogl

5 assemblies

Heteromeric or nucleic-acid complex
7ogk 7ogm 9qh0

3 assemblies

View Construct and Data Evidence
UniProt name PNP_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–549； UniProt 1–549 Author chain B； PDBConstruct 1–549； UniProt 1–549 Author chain C； PDBConstruct 1–549； UniProt 1–549 Author chain G； PDBConstruct 1–549； UniProt 1–549 Author chain I； PDBConstruct 1–549； UniProt 1–549 Author chain K； PDBConstruct 1–549； UniProt 1–549 Author chain M； PDBConstruct 1–549； UniProt 1–549 Author chain O； PDBConstruct 1–549； UniProt 1–549 Author chain R； PDBConstruct 1–549； UniProt 1–549 Author chain T； PDBConstruct 1–549； UniProt 1–549 Author chain V； PDBConstruct 1–549； UniProt 1–549 Author chain X； PDBConstruct 1–549； UniProt 1–549

Ribonuclease E

OrganismNot specified

UniProt P21513

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
10 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
11 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
12 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
14 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
15 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
16 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
2 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
3 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
4 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
6 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
7 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count
8 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1slj 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c 3h1c

13 assemblies; showing the first 12

Homodimer
1smx 1sn8

2 assemblies

Homotetramer
2vmk

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
2bx2 2c0b 2c4r 2fym 2fym 2fym 2vrt 2vrt 2vrt 2vrt 5f6c 5ohg

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name RNE_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 1–41； UniProt 1021–1061 Author chain E； PDBConstruct 1–41； UniProt 1021–1061 Author chain F； PDBConstruct 1–41； UniProt 1021–1061 Author chain H； PDBConstruct 1–41； UniProt 1021–1061 Author chain J； PDBConstruct 1–41； UniProt 1021–1061 Author chain L； PDBConstruct 1–41； UniProt 1021–1061 Author chain N； PDBConstruct 1–41； UniProt 1021–1061 Author chain P； PDBConstruct 1–41； UniProt 1021–1061 Author chain S； PDBConstruct 1–41； UniProt 1021–1061 Author chain U； PDBConstruct 1–41； UniProt 1021–1061 Author chain W； PDBConstruct 1–41； UniProt 1021–1061 Author chain Y； PDBConstruct 1–41； UniProt 1021–1061

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id3h1c
Deposition date deposition_date2009-04-11
Structure title titleCrystal structure of Polynucleotide Phosphorylase (PNPase) core bound to RNase E and Tungstate
Keywords keywords;polynucleotide phosphorylase, RNA turnover, TRANSFERASE, Cytoplasm, Nucleotidyltransferase, RNA-binding, Stress response, Endonuclease, Hydrolase, Nuclease ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3h1c__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3h1c__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3h1c__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）36.39 Å
Rg (electron density)35.52 Å
Total Rg36.09 Å
Atom count12328
Residues1632
Excluded volume219230 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3h1c__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3h1c__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3h1c__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3h1c__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3h1c__assembly_5__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 3h1c__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 3h1c__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 3h1c__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 3h1c__assembly_9__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 3h1c__assembly_10__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
11 1 3h1c__assembly_11__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
12 1 3h1c__assembly_12__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
13 1 3h1c__assembly_13__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
14 1 3h1c__assembly_14__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
15 1 3h1c__assembly_15__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
16 1 3h1c__assembly_16__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

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6. Fold Classification (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

Domain ID domain_id3h1cA01
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_id3h1cA02
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_id3h1cA03
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_id3h1cB01
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_id3h1cB02
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_id3h1cB03
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_id3h1cC01
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_id3h1cC02
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_id3h1cC03
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_id3h1cG01
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_id3h1cG02
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_id3h1cG03
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_id3h1cI01
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_id3h1cI02
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_id3h1cI03
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_id3h1cK01
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_id3h1cK02
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_id3h1cK03
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_id3h1cM01
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_id3h1cM02
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_id3h1cM03
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_id3h1cO01
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_id3h1cO02
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_id3h1cO03
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_id3h1cR01
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_id3h1cR02
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_id3h1cR03
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_id3h1cT01
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_id3h1cT02
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_id3h1cT03
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_id3h1cV01
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_id3h1cV02
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_id3h1cV03
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_id3h1cX01
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_id3h1cX02
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_id3h1cX03
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
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7. Citations (1)