SAXSdb — 6z6o

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

Histone deacetylase HDA1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	HDA1 complex subunit 2 × 4 （Q06629） HDA1 complex subunit 3,HDA1 complex subunit 3 × 4 （Q06623） ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA1_YEAST
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–661； UniProt 40–700 Author chain E； PDBConstruct 1–661； UniProt 40–700 Author chain I； PDBConstruct 1–661； UniProt 40–700 Author chain M； PDBConstruct 1–661； UniProt 40–700 Author chain B； PDBConstruct 1–672； UniProt 29–700 Author chain F； PDBConstruct 1–672； UniProt 29–700 Author chain J； PDBConstruct 1–672； UniProt 29–700 Author chain N； PDBConstruct 1–672； UniProt 29–700

HDA1 complex subunit 2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q06629

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Histone deacetylase HDA1 × 4 （P53973） Histone deacetylase HDA1 × 4 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 4 （Q06623） ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–629； UniProt 10–638 Author chain G； PDBConstruct 1–629； UniProt 10–638 Author chain K； PDBConstruct 1–629； UniProt 10–638 Author chain O； PDBConstruct 1–629； UniProt 10–638

HDA1 complex subunit 3,HDA1 complex subunit 3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q06623

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Histone deacetylase HDA1 × 4 （P53973） Histone deacetylase HDA1 × 4 （P53973） HDA1 complex subunit 2 × 4 （Q06629） ZINC ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA3_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–306； UniProt 28–333 Author chain D； PDBConstruct 307–542； UniProt 404–639 Author chain H； PDBConstruct 1–306； UniProt 28–333 Author chain H； PDBConstruct 307–542； UniProt 404–639 Author chain L； PDBConstruct 1–306； UniProt 28–333 Author chain L； PDBConstruct 307–542； UniProt 404–639 Author chain P； PDBConstruct 1–306； UniProt 28–333 Author chain P； PDBConstruct 307–542； UniProt 404–639

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	6z6o
Deposition date deposition_date	2020-05-28
Structure title title	HDAC-TC
Keywords keywords	Protein complex, GENE REGULATION; GENE REGULATION
Experimental Method method	ELECTRON MICROSCOPY

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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.

6z6o__assembly_1__model_1

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

Download this curve (.dat)

6z6o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z6o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	86.14 Å
Rg (electron density)	85.58 Å
Total Rg	85.67 Å
Atom count	77516
Residues	9628
Excluded volume	1382600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z6o__assembly_1__model_1`	hexadecameric （16）	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 (5)

Entity 1 Entity 1 polymer

Description description	Histone deacetylase HDA1
Molecular weight formula_weight	74852.0 kDa
EC 编号 ec_number	3.5.1.98
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M
Atom count atom_count	77516

RQVIVPVCMPKIHYSPLKTGLCYDVRMRYHAKIFTSYFEYIDPHPEDPRRIYRIYKILAENGLINDPTLSGVDDLGDLMLKIPVRAATSEEILEVHTKEHLEFIESTEKMSREELLKETEKGDSVYFNNDSYASARLPCGGAIEACKAVVEGRVKNSLAVVRPPGHHAEPQAAGGFCLFSNVAVAAKNILKNYPESVRRIMILDWDIHHGNGTQKSFYQDDQVLYVSLHRFEMGKYYPGTIQGQYDQTGEGKGEGFNCNITWPVGGVGDAEYMWAFEQVVMPMGREFKPDLVIISSGFDAADGDTIGQCHVTPSCYGHMTHMLKSLARGNLCVVLEGGYNLDAIARSALSVAKVLIGEPPDELPDPLSDPKPEVIEMIDKVIRLQSKYWNCFRRRHANSGCNFNEPLNDSIISKNFPLQKAIRQQQQHYLSDEFNFVTLPLVSMDLPDNTVLCTPNISESNTIIIVVHDTSDIWAKRNVISGTIDLSSSVIIDNSLDFIKWGLDRKYGIIDVNIPLTLFEPDNYSGMITSQEVLIYLWDNYIKYFPSVAKIAFIGIGDSYSGIVHLLGHRDTRAVTKTVINFLGDKQLKPLVPLVDETLSEWYFKNSLIFSNNSHQCWKENESRKPRKKFGRVLRCDTDGLNNIIEERFEEATDFILDSFE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone deacetylase HDA1
Molecular weight formula_weight	76017.2 kDa
EC 编号 ec_number	3.5.1.98
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

ENSLSTTSKSKRQVIVPVCMPKIHYSPLKTGLCYDVRMRYHAKIFTSYFEYIDPHPEDPRRIYRIYKILAENGLINDPTLSGVDDLGDLMLKIPVRAATSEEILEVHTKEHLEFIESTEKMSREELLKETEKGDSVYFNNDSYASARLPCGGAIEACKAVVEGRVKNSLAVVRPPGHHAEPQAAGGFCLFSNVAVAAKNILKNYPESVRRIMILDWDIHHGNGTQKSFYQDDQVLYVSLHRFEMGKYYPGTIQGQYDQTGEGKGEGFNCNITWPVGGVGDAEYMWAFEQVVMPMGREFKPDLVIISSGFDAADGDTIGQCHVTPSCYGHMTHMLKSLARGNLCVVLEGGYNLDAIARSALSVAKVLIGEPPDELPDPLSDPKPEVIEMIDKVIRLQSKYWNCFRRRHANSGCNFNEPINDSIISKNFPLQKAIRQQQQHYLSDEFNFVTLPLVSMDLPDNTVLCTPNISESNTIIIVVHDTSDIWAKRNVISGTIDLSSSVIIDNSLDFIKWGLDRKYGIIDVNIPLTLFEPDNYSGMITSQEVLIYLWDNYIKYFPSVAKIAFIGIGDSYSGIVHLLGHRDTRAVTKTVINFLGDKQLKPLVPLVDETLSEWYFKNSLIFSNNSHQCWKENESRKPRKKFGRVLRCDTDGLNNIIEERFEEATDFILDSFE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	HDA1 complex subunit 2
Molecular weight formula_weight	71915.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

KVYYLPVTLTQFQKDLSEILISLHAKSFKASIIGEPQADAVNKPSGLPAGPETHPYPTLSQRQLTYIFDSNIRAIANHPSLLVDHYMPRQLLRMEPTESSIAGSHKFQVLNQLINSICFRDREGSPNEVIKCAIIAHSIKELDLLEGLILGKKFRTKRLSGTSLYNEKHKFPNLPTVDSTINKDGTPNSVSSTSSNSNSTSYTGYSKDDYDYSVKRNLKKRKINTDDWLFLATTKHLKHDQYLLANYDIDMIISFDPMLEVELPALQVLRNNANKDIPIIKLLVQNSPDHYLLDSEIKNSSVKSSHLSNNGHVDDSQEYEEIKSSLLYFLQARNAPVNNCEIDYIKLVKCCLEGKDCNNILPVLDLITLDEASKDSSDSGFWQPQLTKLQYSSTELPLWDGPLDIKTYQTELMHRAVIRLRDIQDEYAKGTVPLYEKRLNETQRQNQLDEIKNSVGLTFKKKQEVEKSINDSEKRLKHAMTESTKLQNKINHLLKNRQELENFNKLPSNTISSENHLEEGSALADKLKEYIDKNATLFNKLKELQQANAEKSKLNDELRSKYQIESSKAAESAQTLKILQESMKSLENEVNGPLTKFSTESLKKELERLQNDFQSLKARNKFLKNYITL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	HDA1 complex subunit 3,HDA1 complex subunit 3
Molecular weight formula_weight	63292.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SGDYWLPTTMSLYQKELTDQIVSLHYSDILRYFETSHYKEDVILESMKTMCLNGSLVATHPYLLIDHYMPKSLITRDVPAHLAENSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSKQKANDFSCTVHLFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFGKKFDKNSREYLENVTAAMVILRDRLGTLPPDLRPIYSQKLHYLVEWLENPTVPWPLPDIYPLKQYTSMDVERSLLTEVHFKNSSNVNYHLSSGIITHKLIQSMGEVYMDICVQKQELDDYSCLDDLQNDHLKFFSNEDEKIIKEYETVLRTNNENLNRSHELEVENNLKFSQIETLEKDIETLKGSLMAQGETLSKLKDAFVKTDNVQDEIEKEERVSVSRDTEKKYMEQEIKRAVDAIRENEEETHKLNEKQNGLESELKLKFEKSEISTKELNEKIGFLKKELKLENDLNEELVGQLSKTMDNLENLTIPRVRTQ

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	6z6oA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6oB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6oD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12360 —

Domain ID domain_id	6z6oE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6oF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6oH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12360 —

Domain ID domain_id	6z6oI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6oJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6oL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12360 —

Domain ID domain_id	6z6oM01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6oN01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	800 — Arginase; Chain A
Homologous superfamily homologous superfamily	20 — Histone deacetylase domain

Domain ID domain_id	6z6oP01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12360 —

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	53757

HDAC-TC

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

Histone deacetylase HDA1

State in the Current Structure

Other States of the Same Protein in the Database

HDA1 complex subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

HDA1 complex subunit 3,HDA1 complex subunit 3

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

6z6o__assembly_1__model_1

6z6o__assembly_1__model_1 | I(q)

6z6o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

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

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

HDAC-TC

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

Histone deacetylase HDA1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HDA1 complex subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HDA1 complex subunit 3,HDA1 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6z6o__assembly_1__model_1

6z6o__assembly_1__model_1 | I(q)

6z6o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

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

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)