2e9x

The crystal structure of human GINS core complex

Method: X-RAY DIFFRACTION

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

DNA replication complex GINS protein PSF1

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 replication complex GINS protein PSF2 × 1 （Q9Y248） GINS complex subunit 3 × 1 （Q9BRX5） GINS complex subunit 4 × 1 （Q9BRT9） SULFATE ION × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DNA replication complex GINS protein PSF2 × 1 （Q9Y248） GINS complex subunit 3 × 1 （Q9BRX5） GINS complex subunit 4 × 1 （Q9BRT9） SULFATE ION × 3 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	DNA replication complex GINS protein PSF2 × 2 （Q9Y248） GINS complex subunit 3 × 2 （Q9BRX5） GINS complex subunit 4 × 2 （Q9BRT9） SULFATE ION × 6 water × 8	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 8	DNA replication complex GINS protein PSF2 × 2 （Q9Y248） GINS complex subunit 3 × 2 （Q9BRX5） GINS complex subunit 4 × 2 （Q9BRT9） SULFATE ION × 6 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 1–149 Author chain E； PDBConstruct 1–149； UniProt 1–149

DNA replication complex GINS protein PSF2

Homo sapiens

UniProt Q9Y248

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA replication complex GINS protein PSF1 × 1 （Q14691） GINS complex subunit 3 × 1 （Q9BRX5） GINS complex subunit 4 × 1 （Q9BRT9） SULFATE ION × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DNA replication complex GINS protein PSF1 × 1 （Q14691） GINS complex subunit 3 × 1 （Q9BRX5） GINS complex subunit 4 × 1 （Q9BRT9） SULFATE ION × 3 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	DNA replication complex GINS protein PSF1 × 2 （Q14691） GINS complex subunit 3 × 2 （Q9BRX5） GINS complex subunit 4 × 2 （Q9BRT9） SULFATE ION × 6 water × 8	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 8	DNA replication complex GINS protein PSF1 × 2 （Q14691） GINS complex subunit 3 × 2 （Q9BRX5） GINS complex subunit 4 × 2 （Q9BRT9） SULFATE ION × 6 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PSF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–185； UniProt 1–185 Author chain F； PDBConstruct 1–185； UniProt 1–185

GINS complex subunit 3

Homo sapiens

UniProt Q9BRX5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA replication complex GINS protein PSF1 × 1 （Q14691） DNA replication complex GINS protein PSF2 × 1 （Q9Y248） GINS complex subunit 4 × 1 （Q9BRT9） SULFATE ION × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DNA replication complex GINS protein PSF1 × 1 （Q14691） DNA replication complex GINS protein PSF2 × 1 （Q9Y248） GINS complex subunit 4 × 1 （Q9BRT9） SULFATE ION × 3 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	DNA replication complex GINS protein PSF1 × 2 （Q14691） DNA replication complex GINS protein PSF2 × 2 （Q9Y248） GINS complex subunit 4 × 2 （Q9BRT9） SULFATE ION × 6 water × 8	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 8	DNA replication complex GINS protein PSF1 × 2 （Q14691） DNA replication complex GINS protein PSF2 × 2 （Q9Y248） GINS complex subunit 4 × 2 （Q9BRT9） SULFATE ION × 6 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9BRX5_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–219； UniProt 1–216 Author chain G； PDBConstruct 4–219； UniProt 1–216

GINS complex subunit 4

Homo sapiens

UniProt Q9BRT9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA replication complex GINS protein PSF1 × 1 （Q14691） DNA replication complex GINS protein PSF2 × 1 （Q9Y248） GINS complex subunit 3 × 1 （Q9BRX5） SULFATE ION × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	DNA replication complex GINS protein PSF1 × 1 （Q14691） DNA replication complex GINS protein PSF2 × 1 （Q9Y248） GINS complex subunit 3 × 1 （Q9BRX5） SULFATE ION × 3 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 8	DNA replication complex GINS protein PSF1 × 2 （Q14691） DNA replication complex GINS protein PSF2 × 2 （Q9Y248） GINS complex subunit 3 × 2 （Q9BRX5） SULFATE ION × 6 water × 8	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 8	DNA replication complex GINS protein PSF1 × 2 （Q14691） DNA replication complex GINS protein PSF2 × 2 （Q9Y248） GINS complex subunit 3 × 2 （Q9BRX5） SULFATE ION × 6 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9BRT9_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–223； UniProt 1–223 Author chain H； PDBConstruct 1–223； UniProt 1–223

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	2e9x
Deposition date deposition_date	2007-01-27
Structure title title	The crystal structure of human GINS core complex
Keywords keywords	GINS complex, Eukaryotic DNA replication, REPLICATION; 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.

2e9x__assembly_1__model_1

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

Download this curve (.dat)

2e9x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2e9x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.57 Å
Rg (electron density)	28.82 Å
Total Rg	29.50 Å
Atom count	5732
Residues	702
Excluded volume	102090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2e9x__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2e9x__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2e9x__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2e9x__assembly_4__model_1`	octameric （8）	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 (6)

Entity 1 Entity 1 polymer

Description description	DNA replication complex GINS protein PSF1
Molecular weight formula_weight	17502.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	11975

MFCEKAMELIRELHRAPEGQLPAFNEDGLRQVLEEMKALYEQNQSDVNEAKSGGRSDLIPTIKFRHCSLLRNRRCTVAYLYDRLLRIRALRWEYGSVLPNALRFHMAAEEMEWFNNYKRSLATYMRSLGGDEGLDITQDMKPPKSLYIE

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA replication complex GINS protein PSF2
Molecular weight formula_weight	21453.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDAAEVEFLAEKELVTIIPNFSLDKIYLIGGDLGPFNPGLPVEVPLWLAINLKQRQKCRLLPPEWMDVEKLEKMRDHERKEETFTPMPSPYYMELTKLLLNHASDNIPKADEIRTLVKDMWDTRIAKLRVSADSFVRQQEAHAKLDNLTLMEINTSGTFLTQALNHMYKLRTNLQPLESTQSQDF

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	GINS complex subunit 3
Molecular weight formula_weight	24854.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPHMSEAYFRVESGALGPEENFLSLDDILMSHEKLPVRTETAMPRLGAFFLERSAGAETDNAVPQGSKLELPLWLAKGLFDNKRRILSVELPKIYQEGWRTVFSADPNVVDLHKMGPHFYGFGSQLLHFDSPENADISQSLLQTFIGRFRRIMDSSQNAYNEDTSALVARLDEMERGLFQTGQKGLNDFQCWEKGQASQITASNLVQNYKKRKFTDMED

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 BL21(DE3)

Entity 4 Entity 4 polymer

Description description	GINS complex subunit 4
Molecular weight formula_weight	26081.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTEEVDFLGQDSDGGSEEVVLTPAELIERLEQAWMNEKFAPELLESKPEIVECVMEQLEHMEENLRRAKREDLKVSIHQMEMERIRYVLSSYLRCRLMKIEKFFPHVLEKEKTRPEGEPSSLSPEELAFAREFMANTESYLKNVALKHMPPNLQKVDLFRAVPKPDLDSYVFLRVRERQENILVEPDTDEQRDYVIDLEKGSQHLIRYKTIAPLVASGAVQLI

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 BL21(DE3)

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	532

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6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d2e9xa1
Class class	a — All alpha proteins
Fold Fold fold	a.278 — GINS helical bundle-like
Superfamily Superfamily superfamily	a.278.1 — GINS helical bundle-like
Family Family family	a.278.1.1 — PSF1 N-terminal domain-like

Domain ID domain_id	d2e9xb1
Class class	a — All alpha proteins
Fold Fold fold	a.278 — GINS helical bundle-like
Superfamily Superfamily superfamily	a.278.1 — GINS helical bundle-like
Family Family family	a.278.1.2 — PSF2 C-terminal domain-like

Domain ID domain_id	d2e9xb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.344 — GINS/PriA/YqbF domain
Superfamily Superfamily superfamily	d.344.1 — PriA/YqbF domain
Family Family family	d.344.1.0 — automated matches

Domain ID domain_id	d2e9xc1
Class class	a — All alpha proteins
Fold Fold fold	a.278 — GINS helical bundle-like
Superfamily Superfamily superfamily	a.278.1 — GINS helical bundle-like
Family Family family	a.278.1.3 — PSF3 C-terminal domain-like

Domain ID domain_id	d2e9xc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.344 — GINS/PriA/YqbF domain
Superfamily Superfamily superfamily	d.344.1 — PriA/YqbF domain
Family Family family	d.344.1.4 — PSF3 N-terminal domain-like

Domain ID domain_id	d2e9xc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2e9xd1
Class class	a — All alpha proteins
Fold Fold fold	a.278 — GINS helical bundle-like
Superfamily Superfamily superfamily	a.278.1 — GINS helical bundle-like
Family Family family	a.278.1.4 — SLD5 N-terminal domain-like

Domain ID domain_id	d2e9xd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.344 — GINS/PriA/YqbF domain
Superfamily Superfamily superfamily	d.344.1 — PriA/YqbF domain
Family Family family	d.344.1.3 — SLD5 C-terminal domain-like

Domain ID domain_id	d2e9xe_
Class class	a — All alpha proteins
Fold Fold fold	a.278 — GINS helical bundle-like
Superfamily Superfamily superfamily	a.278.1 — GINS helical bundle-like
Family Family family	a.278.1.1 — PSF1 N-terminal domain-like

Domain ID domain_id	d2e9xf1
Class class	a — All alpha proteins
Fold Fold fold	a.278 — GINS helical bundle-like
Superfamily Superfamily superfamily	a.278.1 — GINS helical bundle-like
Family Family family	a.278.1.2 — PSF2 C-terminal domain-like

Domain ID domain_id	d2e9xf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.344 — GINS/PriA/YqbF domain
Superfamily Superfamily superfamily	d.344.1 — PriA/YqbF domain
Family Family family	d.344.1.0 — automated matches

Domain ID domain_id	d2e9xg1
Class class	a — All alpha proteins
Fold Fold fold	a.278 — GINS helical bundle-like
Superfamily Superfamily superfamily	a.278.1 — GINS helical bundle-like
Family Family family	a.278.1.3 — PSF3 C-terminal domain-like

Domain ID domain_id	d2e9xg2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.344 — GINS/PriA/YqbF domain
Superfamily Superfamily superfamily	d.344.1 — PriA/YqbF domain
Family Family family	d.344.1.4 — PSF3 N-terminal domain-like

Domain ID domain_id	d2e9xh1
Class class	a — All alpha proteins
Fold Fold fold	a.278 — GINS helical bundle-like
Superfamily Superfamily superfamily	a.278.1 — GINS helical bundle-like
Family Family family	a.278.1.4 — SLD5 N-terminal domain-like

Domain ID domain_id	d2e9xh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.344 — GINS/PriA/YqbF domain
Superfamily Superfamily superfamily	d.344.1 — PriA/YqbF domain
Family Family family	d.344.1.3 — SLD5 C-terminal domain-like

CATH v4.4 (12 domains)

Domain ID domain_id	2e9xA01
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	1030 —

Domain ID domain_id	2e9xB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2e9xB02
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	1020 —

Domain ID domain_id	2e9xC00
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	2050 —

Domain ID domain_id	2e9xD01
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	1030 —

Domain ID domain_id	2e9xD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	2e9xE01
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	1030 —

Domain ID domain_id	2e9xF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2e9xF02
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	1020 —

Domain ID domain_id	2e9xG00
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	2050 —

Domain ID domain_id	2e9xH01
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	1030 —

Domain ID domain_id	2e9xH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	5 — Ribosomal Protein L9; domain 1
Homologous superfamily homologous superfamily	60 —

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Unit-cell length a length_a	57.928 Å
Unit-cell length b length_b	88.741 Å
Unit-cell length c length_c	102.129 Å
Unit-cell angle α angle_alpha	104.69 °
Unit-cell angle β angle_beta	102.96 °
Unit-cell angle γ angle_gamma	95.47 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.820 Å
R factor r_factor	0.1990
R_work r_work	0.1970
R_free r_free	0.2330

The crystal structure of human GINS core complex

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

DNA replication complex GINS protein PSF1

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 complex GINS protein PSF2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GINS complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GINS complex subunit 4

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

2e9x__assembly_1__model_1

2e9x__assembly_1__model_1 | I(q)

2e9x__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

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

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

CATH v4.4 (12 domains)

7. Citations (1)