SAXSdb — 2zxx

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

Geminin

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA replication factor Cdt1 × 1 （Q8R4E9） water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DNA replication factor Cdt1 × 1 （Q8R4E9） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GEMI_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–79； UniProt 79–157 Author chain B； PDBConstruct 1–79； UniProt 79–157 Author chain D； PDBConstruct 1–79； UniProt 79–157 Author chain E； PDBConstruct 1–79； UniProt 79–157

DNA replication factor Cdt1

Mus musculus

UniProt Q8R4E9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Geminin × 2 （O88513） water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Geminin × 2 （O88513） water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDT1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–197； UniProt 172–368 Author chain F； PDBConstruct 1–197； UniProt 172–368

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	2zxx
Deposition date deposition_date	2009-01-08
Structure title title	Crystal structure of Cdt1/geminin complex
Keywords keywords	;COILED-COIL, Cell cycle, Coiled coil, DNA replication inhibitor, Phosphoprotein, DNA replication, DNA-binding, Nucleus, Proto-oncogene, Ubl conjugation, CELL CYCLE-REPLICATION COMPLEX ;; CELL CYCLE/REPLICATION
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.

2zxx__assembly_1__model_1

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

Download this curve (.dat)

2zxx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zxx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.20 Å
Rg (electron density)	28.88 Å
Total Rg	29.35 Å
Atom count	2755
Residues	325
Excluded volume	49024 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zxx__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zxx__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 (3)

Entity 1 Entity 1 polymer

Description description	Geminin
Molecular weight formula_weight	9466.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	5476

TQEAFDLISKENPSSQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYMAEVIERLSN

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA replication factor Cdt1
Molecular weight formula_weight	23080.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TEQPCVEKAPAYQRFHALAQPGLPGLVLPYKYQVLVEMFRSMDTIVSMLHNRSETVTFAKVKQGVQEMMRKRFEERNVGQIKTVYPTSYRFRQECNVPTFKDSIKRSDYQLTIEPLLGQEAGGATQLTATCLLQRRQVFRQNLVERVKEQHKVFLASLNPPMAVPDDQLTRWHPRFNVDEVPDIEPAELPQPPVTEK

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2zxxa_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.28 — Geminin coiled-coil domain
Family Family family	h.1.28.1 — Geminin coiled-coil domain

Domain ID domain_id	d2zxxb_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.28 — Geminin coiled-coil domain
Family Family family	h.1.28.1 — Geminin coiled-coil domain

Domain ID domain_id	d2zxxc_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.52 — DNA replication factor Cdt1

Domain ID domain_id	d2zxxd_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.28 — Geminin coiled-coil domain
Family Family family	h.1.28.1 — Geminin coiled-coil domain

Domain ID domain_id	d2zxxe_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.28 — Geminin coiled-coil domain
Family Family family	h.1.28.1 — Geminin coiled-coil domain

Domain ID domain_id	d2zxxf_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.52 — DNA replication factor Cdt1

CATH v4.4 (4 domains)

Domain ID domain_id	2zxxA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1180 — Geminin coiled-coil domain

Domain ID domain_id	2zxxB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1180 — Geminin coiled-coil domain

Domain ID domain_id	2zxxD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1180 — Geminin coiled-coil domain

Domain ID domain_id	2zxxE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1180 — Geminin coiled-coil domain

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Unit-cell length a length_a	113.769 Å
Unit-cell length b length_b	94.334 Å
Unit-cell length c length_c	115.572 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2371
R_work r_work	0.2349
R_free r_free	0.2774

Crystal structure of Cdt1/geminin complex

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

Geminin

State in the Current Structure

Other States of the Same Protein in the Database

DNA replication factor Cdt1

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

2zxx__assembly_1__model_1

2zxx__assembly_1__model_1 | I(q)

2zxx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Cdt1/geminin complex

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

Geminin

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 replication factor Cdt1

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

2zxx__assembly_1__model_1

2zxx__assembly_1__model_1 | I(q)

2zxx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)