SAXSdb — 1yvl

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

Signal transducer and activator of transcription 1-alpha/beta

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–683	Fragment：residues 1-683	5-residue peptide × 1 AU GOLD ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；HEPES, PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.281
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–683	Fragment：residues 1-683	5-residue peptide × 1 AU GOLD ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；HEPES, PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.281
3	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–683 Chain B； UniProt 1–683	Fragment：residues 1-683	5-residue peptide × 4 AU GOLD ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；HEPES, PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.281
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–683 Chain B； UniProt 1–683	Fragment：residues 1-683	5-residue peptide × 2 AU GOLD ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；HEPES, PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.281

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 1YVL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BF5 TYROSINE PHOSPHORYLATED STAT-1/DNA COMPLEX Deposited 1998-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 136–683（548 aa） Fragment：RESIDUES 136-710	Mutation：PHOSPHORYLATED TYR 701 Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K	Resolution 2.90 Å R-free 0.293
2KA6 NMR structure of the CBP-TAZ2/STAT1-TAD complex Deposited 2008-10-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 710–750（41 aa） Fragment：UNP residues 710 to 750	Not recorded	ZN ZINC ION × 3	SOLUTION NMR NMR measurement conditions pH 6.8；290 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition 1 mM [U-100% 15N] TAZ2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3WWT Crystal Structure of the Y3:STAT1ND complex Deposited 2014-06-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa） Fragment：N-terminal domain, UNP residues 1-126	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；30% PEG400, 0.2M CaCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.237
7NUF Vaccinia virus protein 018 in complex with STAT1 Deposited 2021-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 132–684（553 aa）	Mutation：Delta183-190, H182A, E393A, E394A	SO4 SULFATE ION × 1 ACE ACETYL GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；300:300 nl drop of protein:condition Protein: 10 mg/ml STAT1:peptide complex in 20 mM Tris pH8.0, 300 mM NaCl, 1 mM EDTA, 5 mM TCEP Condition: 16% PEG 3350 (w/v), 175 mM KCl, 125 mM NH4SO4,	Resolution 2.00 Å R-free 0.256
8D3F Crystal structure of human STAT1 in complex with the repeat region from Toxoplasma protein TgIST Deposited 2022-06-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 132–713（582 aa） Fragment：STAT1-binding region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.3-6.0, 3 M sodium chloride and 50 mM sodium citrate tribasic	Resolution 2.97 Å R-free 0.288
8YYU A tetrameric STAT1-DNA complex Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: dodecameric	Chain A 1–750（750 aa） Chain D 1–750（750 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8YYU A tetrameric STAT1-DNA complex Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–750（750 aa） Chain D 1–750（750 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8YYU A tetrameric STAT1-DNA complex Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–750（750 aa） Chain D 1–750（750 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8YYV A dimeric STAT1-DNA complex Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric	Chain A 1–750（750 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
8YYV A dimeric STAT1-DNA complex Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–750（750 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
8YYV A dimeric STAT1-DNA complex Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–750（750 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
9IFX Beta-hairpin macrocyclic peptide in complex with STAT1 Deposited 2025-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 132–684（553 aa）	Not recorded	OXE ORTHO-XYLENE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallisation condition: 4% v/v TacsimateTM pH 5.0 12% w/v Polyethylene glycol 3,350 Protein:peptide complex: 5 mg /ml 20 mM Tris pH 8.0, 300 mM NaCl	Resolution 3.64 Å R-free 0.271
9IGA Beta-hairpin macrocyclic peptide in complex with STAT1 Deposited 2025-02-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 132–684（553 aa）	Mutation：132-684,delta183-190,H182A,E393A,E394A	OXE ORTHO-XYLENE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallisation conditions: 0.1 M Bis-Tris 5.5 0.2 M Ammonium acetate 25 % w/v PEG 3350 Protein:peptide complex: 5 mg ml 20 mM Tris pH 8.0, 300 mM NaCl	Resolution 2.80 Å R-free 0.313

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STAT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–683； UniProt 1–683 Author chain B； PDBConstruct 1–683； UniProt 1–683

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	1yvl
Deposition date deposition_date	2005-02-16
Structure title title	Structure of Unphosphorylated STAT1
Keywords keywords	SIGNALING PROTEIN; SIGNALING 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	45.95 Å
Radius of gyration Rg (electron density) rg_electron	45.99 Å
Forward intensity I(0) i0	346691000.00
Molecular weight molecular_weight	154490.0 kDa
Excluded volume excluded_volume	193940 Å³
Envelope volume envelope_volume	290790 Å³
Hydration-shell volume shell_volume	55307 Å³
Envelope diameter envelope_diameter	169.1 Å
Shell Rg shell_rg	48.31 Å
Envelope Rg envelope_rg	44.24 Å
Shape Rg shape_rg	46.04 Å
Total Rg total_rg	45.91 Å
Total atoms total_atoms	10863
Residues n_residues	1313
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	160.4 Å
Rg (real space) rg_real	46.17 Å
Rg uncertainty (real space) rg_real_error	2.36 Å
I(0) (real space) i0_real	3.4670e+08
I(0) uncertainty (real space) i0_real_error	7.8040e+06
Rg (reciprocal space) rg_reciprocal	45.95 Å
I(0) (reciprocal space) i0_reciprocal	346600000.0000
Solution quality estimate total_estimate	0.8609
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	51.9 Å
Skewness Skewness skewness	0.423
Kurtosis Kurtosis kurtosis	-0.303
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14550000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.833

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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	Signal transducer and activator of transcription 1-alpha/beta
Molecular weight formula_weight	80044.3 kDa
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	10863

MSQWYELQQLDSKFLEQVHQLYDDSFPMEIRQYLAQWLEKQDWEHAANDVSFATIRFHDLLSQLDDQYSRFSLENNFLLQHNIRKSKRNLQDNFQEDPIQMSMIIYSCLKEERKILENAQRFNQAQSGNIQSTVMLDKQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQLLLKKMYLMLDNKRKEVVHKIIELLNVTELTQNALINDELVEWKRRQQSACIGGPPNACLDQLQNWFTIVAESLQQVRQQLKKLEELEQKYTYEHDPITKNKQVLWDRTFSLFQQLIQSSFVVERQPCMPTHPQRPLVLKTGVQFTVKLRLLVKLQELNYNLKVKVLFDKDVNERNTVKGFRKFNILGTHTKVMNMEESTNGSLAAEFRHLQLKEQKNAGTRTNEGPLIVTEELHSLSFETQLCQPGLVIDLETTSLPVVVISNVSQLPSGWASILWYNMLVAEPRNLSFFLTPPCARWAQLSEVLSWQFSSVTKRGLNVDQLNMLGEKLLGPNASPDGLIPWTRFCKENINDKNFPFWLWIESILELIKKHLLPLWNDGCIMGFISKERERALLKDQQPGTFLLRFSESSREGAITFTWVERSQNGGEPDFHAVEPYTKKELSAVTFPDIIRNYKVMAAENIPENPLKYLYPNIDKDHAFGKYYSR

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	5-residue peptide
Molecular weight formula_weight	740.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

YDKPH

Entity 3 Entity 3 non-polymer

Description description	GOLD ION
Molecular weight formula_weight	197.0 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	1yvlA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	532 — Transcription Factor, Stat-4
Homologous superfamily homologous superfamily	10 — STAT transcription factor, N-terminal domain

Domain ID domain_id	1yvlA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	20 — STAT transcription factor, all-alpha domain

Domain ID domain_id	1yvlA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	630 — STAT transcription factor, DNA-binding domain

Domain ID domain_id	1yvlA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1yvlA05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	1yvlB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	532 — Transcription Factor, Stat-4
Homologous superfamily homologous superfamily	10 — STAT transcription factor, N-terminal domain

Domain ID domain_id	1yvlB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	20 — STAT transcription factor, all-alpha domain

Domain ID domain_id	1yvlB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	630 — STAT transcription factor, DNA-binding domain

Domain ID domain_id	1yvlB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	1yvlB05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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8. Citations (1)

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Unit-cell length a length_a	102.553 Å
Unit-cell length b length_b	102.553 Å
Unit-cell length c length_c	646.481 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	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2400
R_free r_free	0.2810

fit	/app/data/saxs_computation/yv/1yvl/1yvl.fit
pddf	/app/data/pr_computation/yv/1yvl/1yvl.pr.out
profile	/app/data/saxs_computation/yv/1yvl/1yvl.dat

Structure of Unphosphorylated STAT1

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

Signal transducer and activator of transcription 1-alpha/beta

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

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)