SAXSdb — 4ba9

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 4	MAGNESIUM ION × 5 NICKEL (II) ION × 6 water × 4	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 4	MAGNESIUM ION × 6 NICKEL (II) ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PLOK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–17； UniProt 563–575 Author chain B； PDBConstruct 5–17； UniProt 563–575 Author chain C； PDBConstruct 5–17； UniProt 563–575 Author chain D； PDBConstruct 5–17； UniProt 563–575 Author chain E； PDBConstruct 5–17； UniProt 563–575 Author chain F； PDBConstruct 5–17； UniProt 563–575

DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1

HOMO SAPIENS

UniProt Q9UBZ9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 4	MAGNESIUM ION × 5 NICKEL (II) ION × 6 water × 4	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 4	MAGNESIUM ION × 6 NICKEL (II) ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	REV1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 30–114； UniProt 1157–1241 Author chain B； PDBConstruct 30–114； UniProt 1157–1241 Author chain C； PDBConstruct 30–114； UniProt 1157–1241 Author chain D； PDBConstruct 30–114； UniProt 1157–1241 Author chain E； PDBConstruct 30–114； UniProt 1157–1241 Author chain F； PDBConstruct 30–114； UniProt 1157–1241

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_id	4ba9
Deposition date deposition_date	2012-09-12
Structure title title	The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1
Keywords keywords	TRANSFERASE, TLS, DNA REPAIR; TRANSFERASE
Experimental Method method	X-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.

4ba9__assembly_1__model_1

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

Download this curve (.dat)

4ba9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ba9__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.39 Å
Rg (electron density)	23.53 Å
Total Rg	24.24 Å
Atom count	3433
Residues	419
Excluded volume	61719 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ba9__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ba9__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1
Molecular weight formula_weight	13040.8 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	5313

GPHMHKKSFFDKKRSERGSDAGSAGDGASNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQ

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4ba9A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1280 — DNA repair protein Rev1, C-terminal domain

Domain ID domain_id	4ba9B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1280 — DNA repair protein Rev1, C-terminal domain

Domain ID domain_id	4ba9C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1280 — DNA repair protein Rev1, C-terminal domain

Domain ID domain_id	4ba9D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1280 — DNA repair protein Rev1, C-terminal domain

Domain ID domain_id	4ba9E00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1280 — DNA repair protein Rev1, C-terminal domain

Domain ID domain_id	4ba9F00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	1280 — DNA repair protein Rev1, C-terminal domain

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Unit-cell length a length_a	105.750 Å
Unit-cell length b length_b	105.750 Å
Unit-cell length c length_c	424.270 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	108

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.730 Å
Low-resolution limit resolution_low	42.820 Å
R factor r_factor	0.2162
R_work r_work	0.2144
R_free r_free	0.2501

The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1

State in the Current Structure

Other States of the Same Protein in the Database

DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ba9__assembly_1__model_1

4ba9__assembly_1__model_1 | I(q)

4ba9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

The structural basis for the coordination of Y-family Translesion DNA Polymerases by Rev1

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA POLYMERASE KAPPA, DNA REPAIR PROTEIN REV1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ba9__assembly_1__model_1

4ba9__assembly_1__model_1 | I(q)

4ba9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)