SAXSdb — 4gk5

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

Mitotic spindle assembly checkpoint protein MAD2B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase zeta catalytic subunit × 1 （O60673） DNA repair protein REV1 × 1 （Q9UBZ9） DNA polymerase kappa × 1 （Q9UBT6）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase zeta catalytic subunit × 1 （O60673） DNA repair protein REV1 × 1 （Q9UBZ9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MD2L2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–227； UniProt 1–211 Author chain B； PDBConstruct 17–227； UniProt 1–211

DNA polymerase zeta catalytic subunit

Homo sapiens

UniProt O60673

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Mitotic spindle assembly checkpoint protein MAD2B × 1 （Q9UI95） DNA repair protein REV1 × 1 （Q9UBZ9） DNA polymerase kappa × 1 （Q9UBT6）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Mitotic spindle assembly checkpoint protein MAD2B × 1 （Q9UI95） DNA repair protein REV1 × 1 （Q9UBZ9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOLZ_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–52； UniProt 1847–1898 Author chain D； PDBConstruct 1–52； UniProt 1847–1898

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	Protein heterocomplex	Heteromer	Protein 4	Mitotic spindle assembly checkpoint protein MAD2B × 1 （Q9UI95） DNA polymerase zeta catalytic subunit × 1 （O60673） DNA polymerase kappa × 1 （Q9UBT6）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Mitotic spindle assembly checkpoint protein MAD2B × 1 （Q9UI95） DNA polymerase zeta catalytic subunit × 1 （O60673）	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	3
Chains and sequence ranges	Author chain E； PDBConstruct 2–136； UniProt 1117–1251 Author chain F； PDBConstruct 2–136； UniProt 1117–1251

DNA polymerase kappa

OrganismNot specified

UniProt Q9UBT6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Mitotic spindle assembly checkpoint protein MAD2B × 1 （Q9UI95） DNA polymerase zeta catalytic subunit × 1 （O60673） DNA repair protein REV1 × 1 （Q9UBZ9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLK_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 1–10； UniProt 564–573

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	4gk5
Deposition date deposition_date	2012-08-10
Structure title title	Crystal structure of human Rev3-Rev7-Rev1-Polkappa complex
Keywords keywords	;translesion polymerases complex, four-helix bundle, beta-hairpin domain, anti-parallel sheets, translesion DNA synthesis, polymerase switch, none, TRANSFERASE ;; 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.

4gk5__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4gk5__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4gk5__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.92 Å
Rg (electron density)	20.92 Å
Total Rg	21.84 Å
Atom count	2453
Residues	303
Excluded volume	44435 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4gk5__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4gk5__assembly_2__model_1`	trimeric （3）	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	Mitotic spindle assembly checkpoint protein MAD2B
Molecular weight formula_weight	26960.0 kDa
Mutation mutation	R124A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5058

MGSSHHHHHHSQDPNSMTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLAAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKGSGSGSGSGSGSH

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 polymer

Description description	DNA polymerase zeta catalytic subunit
Molecular weight formula_weight	5632.3 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MLTPTPDSSPRSTSSPSQSKNGSFTPRTANILKPLMSPPSREEIMATLLDHD

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 3 Entity 3 polymer

Description description	DNA repair protein REV1
Molecular weight formula_weight	15179.4 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MLKHEGPPAEKPLEELSASTSGVPGLSSLQSDPAGCVRPPAPNLAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQQSVESVWNMAFDFILDNVQVVLQQTYGSTLKVT

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 4 Entity 4 polymer

Description description	DNA polymerase kappa
Molecular weight formula_weight	1275.5 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

KKSFFDKKRS

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4gk5A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	4gk5B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	4gk5E00
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	4gk5F00
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	119.998 Å
Unit-cell length b length_b	72.762 Å
Unit-cell length c length_c	104.653 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.210 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2341
R_work r_work	0.2315
R_free r_free	0.2810

Crystal structure of human Rev3-Rev7-Rev1-Polkappa complex

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

Mitotic spindle assembly checkpoint protein MAD2B

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase zeta catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

DNA repair protein REV1

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase kappa

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

4gk5__assembly_2__model_1

4gk5__assembly_2__model_1 | I(q)

4gk5__assembly_2__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of human Rev3-Rev7-Rev1-Polkappa complex

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

Mitotic spindle assembly checkpoint protein MAD2B

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 zeta catalytic subunit

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 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

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

4gk5__assembly_2__model_1

4gk5__assembly_2__model_1 | I(q)

4gk5__assembly_2__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)