SAXSdb — 4dhx

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

80 kDa MCM3-associated protein

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1163–1235	Fragment：ENY2-binding region residues 1163-1235	Enhancer of yellow 2 transcription factor homolog × 2 （Q9NPA8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；11% PEG 8000, 0.2M NaOAc, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.250
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1163–1235	Fragment：ENY2-binding region residues 1163-1235	Enhancer of yellow 2 transcription factor homolog × 2 （Q9NPA8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；11% PEG 8000, 0.2M NaOAc, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.250

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4DHX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8R7J Cryo-EM structure of the human TREX-2 complex Deposited 2023-11-25	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 582–1004（423 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8R7K Cryo-EM structure of the human UAP56 - TREX-2 complex Deposited 2023-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 582–1004（423 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9DLP Cryo-EM structure of human TREX-2 complex bound to DDX39B(UAP56) Deposited 2024-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 358–1000（643 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å
9T6N Cryo-EM structure of the human GANP-PCID2-DSS1 complex bound to UAP56 Deposited 2025-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 598–998（401 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.00 Å
9UPB Structure of the human TREX-2 bound to UAP56 Deposited 2025-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 580–1000（421 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；25 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
9UPC Structure of human TREX-2 Deposited 2025-04-28	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 580–1000（421 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；25 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MCM3A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–75； UniProt 1163–1235 Author chain D； PDBConstruct 3–75； UniProt 1163–1235

Enhancer of yellow 2 transcription factor homolog

Homo sapiens

UniProt Q9NPA8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–101 Chain C； UniProt 1–101	Not recorded	80 kDa MCM3-associated protein × 1 （O60318）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；11% PEG 8000, 0.2M NaOAc, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.250
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 1–101 Chain F； UniProt 1–101	Not recorded	80 kDa MCM3-associated protein × 1 （O60318）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；11% PEG 8000, 0.2M NaOAc, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.250

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ENY2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–101； UniProt 1–101 Author chain C； PDBConstruct 1–101； UniProt 1–101 Author chain E； PDBConstruct 1–101； UniProt 1–101 Author chain F； PDBConstruct 1–101； UniProt 1–101

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	4dhx
Deposition date deposition_date	2012-01-30
Structure title title	ENY2:GANP complex
Keywords keywords	mRNA export, TRANSPORT PROTEIN-DNA binding Protein complex; TRANSPORT PROTEIN/DNA binding Protein
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.71 Å
Radius of gyration Rg (electron density) rg_electron	36.14 Å
Forward intensity I(0) i0	53160400.00
Molecular weight molecular_weight	57999.0 kDa
Excluded volume excluded_volume	72878 Å³
Envelope volume envelope_volume	105490 Å³
Hydration-shell volume shell_volume	26273 Å³
Envelope diameter envelope_diameter	134.2 Å
Shell Rg shell_rg	39.20 Å
Envelope Rg envelope_rg	35.51 Å
Shape Rg shape_rg	36.17 Å
Total Rg total_rg	36.27 Å
Total atoms total_atoms	8309
Residues n_residues	508
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	125.8 Å
Rg (real space) rg_real	36.07 Å
Rg uncertainty (real space) rg_real_error	1.80 Å
I(0) (real space) i0_real	5.3160e+07
I(0) uncertainty (real space) i0_real_error	9.8320e+05
Rg (reciprocal space) rg_reciprocal	35.85 Å
I(0) (reciprocal space) i0_reciprocal	53150000.0000
Solution quality estimate total_estimate	0.8250
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.3 Å
Skewness Skewness skewness	0.483
Kurtosis Kurtosis kurtosis	-0.430
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3221000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.747; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.581; Smooth: 0.900

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	80 kDa MCM3-associated protein
Molecular weight formula_weight	8555.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	8559

GSLVLSELSQGLAVELMERVMMEFVRETCSQELKNAVETDQRVRVARCCEDVCAHLVDLFLVEEIFQTAKETLQE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Enhancer of yellow 2 transcription factor homolog
Molecular weight formula_weight	11551.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MVVSKMNKDAQMRAAINQKLIETGERERLKELLRAKLIECGWKDQLKAHCKEVIKEKGLEHVTVDDLVAEITPKGRALVPDSVKKELLQRIRTFLAQHASL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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	250

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4dhxa_
Class class	j — Peptides
Fold Fold fold	j.135 — Sac3 CID region-like
Superfamily Superfamily superfamily	j.135.1 — Sac3 CID region-like
Family Family family	j.135.1.1 — Sac3 CID region-like

Domain ID domain_id	d4dhxb_
Class class	a — All alpha proteins
Fold Fold fold	a.301 — Sus1-like
Superfamily Superfamily superfamily	a.301.1 — Sus1-like
Family Family family	a.301.1.1 — Sus1-like

Domain ID domain_id	d4dhxc_
Class class	a — All alpha proteins
Fold Fold fold	a.301 — Sus1-like
Superfamily Superfamily superfamily	a.301.1 — Sus1-like
Family Family family	a.301.1.1 — Sus1-like

Domain ID domain_id	d4dhxd_
Class class	j — Peptides
Fold Fold fold	j.135 — Sac3 CID region-like
Superfamily Superfamily superfamily	j.135.1 — Sac3 CID region-like
Family Family family	j.135.1.1 — Sac3 CID region-like

Domain ID domain_id	d4dhxe_
Class class	a — All alpha proteins
Fold Fold fold	a.301 — Sus1-like
Superfamily Superfamily superfamily	a.301.1 — Sus1-like
Family Family family	a.301.1.1 — Sus1-like

Domain ID domain_id	d4dhxf_
Class class	a — All alpha proteins
Fold Fold fold	a.301 — Sus1-like
Superfamily Superfamily superfamily	a.301.1 — Sus1-like
Family Family family	a.301.1.1 — Sus1-like

CATH v4.4 (6 domains)

Domain ID domain_id	4dhxA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1340 —

Domain ID domain_id	4dhxB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	140 — ENY2/SUS1

Domain ID domain_id	4dhxC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	140 — ENY2/SUS1

Domain ID domain_id	4dhxD00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1340 —

Domain ID domain_id	4dhxE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	140 — ENY2/SUS1

Domain ID domain_id	4dhxF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	140 — ENY2/SUS1

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8. Citations (1)

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Unit-cell length a length_a	68.592 Å
Unit-cell length b length_b	76.124 Å
Unit-cell length c length_c	70.612 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.884 Å
R factor r_factor	0.2239
R_work r_work	0.2224
R_free r_free	0.2504

fit	/app/data/saxs_computation/dh/4dhx/4dhx.fit
pddf	/app/data/pr_computation/dh/4dhx/4dhx.pr.out
profile	/app/data/saxs_computation/dh/4dhx/4dhx.dat

ENY2:GANP complex

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

80 kDa MCM3-associated protein

State in the Current Structure

Other States of the Same Protein in the Database

Enhancer of yellow 2 transcription factor homolog

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)