6z6p

HDAC-PC-Nuc

Method: ELECTRON MICROSCOPY

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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–DNA	Heteromer	Protein 12 DNA 2	HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） Histone H3 × 1 （A0A310TTQ1） Histone H4 × 1 （P62799） Histone H2A × 1 （Q6AZJ8） Histone H2B × 1 （A0A1L8FQA5） Histone H3.2 × 1 （P84233） Histone H4 × 1 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

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 K； PDBConstruct 1–661； UniProt 40–700 Author chain L； PDBConstruct 1–672； UniProt 29–700

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–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 2 × 1 （Q06629） Histone H3 × 1 （A0A310TTQ1） Histone H4 × 1 （P62799） Histone H2A × 1 （Q6AZJ8） Histone H2B × 1 （A0A1L8FQA5） Histone H3.2 × 1 （P84233） Histone H4 × 1 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–307； UniProt 28–334 Author chain M； PDBConstruct 308–543； UniProt 404–639

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–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） Histone H3 × 1 （A0A310TTQ1） Histone H4 × 1 （P62799） Histone H2A × 1 （Q6AZJ8） Histone H2B × 1 （A0A1L8FQA5） Histone H3.2 × 1 （P84233） Histone H4 × 1 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA2_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain N； PDBConstruct 1–629； UniProt 10–638

Histone H3

Xenopus laevis

UniProt A0A310TTQ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） Histone H4 × 1 （P62799） Histone H2A × 1 （Q6AZJ8） Histone H2B × 1 （A0A1L8FQA5） Histone H3.2 × 1 （P84233） Histone H4 × 1 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A310TTQ1_XENLA
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain A； PDBConstruct 1–97； UniProt 39–135

Histone H4

Xenopus laevis

UniProt P62799

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） Histone H3 × 1 （A0A310TTQ1） Histone H2A × 1 （Q6AZJ8） Histone H2B × 1 （A0A1L8FQA5） Histone H3.2 × 1 （P84233） Histone H2A type 1 × 1 （P06897） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_XENLA
Isoform	—
PDB entities	6, 10
Chains and sequence ranges	Author chain B； PDBConstruct 1–83； UniProt 21–103 Author chain F； PDBConstruct 1–78； UniProt 26–103

Histone H2A

Xenopus laevis

UniProt Q6AZJ8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） Histone H3 × 1 （A0A310TTQ1） Histone H4 × 1 （P62799） Histone H2B × 1 （A0A1L8FQA5） Histone H3.2 × 1 （P84233） Histone H4 × 1 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6AZJ8_XENLA
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain C； PDBConstruct 1–103； UniProt 17–119

Histone H2B

Xenopus laevis

UniProt A0A1L8FQA5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） Histone H3 × 1 （A0A310TTQ1） Histone H4 × 1 （P62799） Histone H2A × 1 （Q6AZJ8） Histone H3.2 × 1 （P84233） Histone H4 × 1 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1L8FQA5_XENLA
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain D； PDBConstruct 1–95； UniProt 32–126

Histone H3.2

Xenopus laevis

UniProt P84233

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） Histone H3 × 1 （A0A310TTQ1） Histone H4 × 1 （P62799） Histone H2A × 1 （Q6AZJ8） Histone H2B × 1 （A0A1L8FQA5） Histone H4 × 1 （P62799） Histone H2A type 1 × 1 （P06897） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H32_XENLA
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain E； PDBConstruct 1–97； UniProt 40–136

Histone H2A type 1

Xenopus laevis

UniProt P06897

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） Histone H3 × 1 （A0A310TTQ1） Histone H4 × 1 （P62799） Histone H2A × 1 （Q6AZJ8） Histone H2B × 1 （A0A1L8FQA5） Histone H3.2 × 1 （P84233） Histone H4 × 1 （P62799） Histone H2B × 1 （A0A1L8FQ56） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1_XENLA
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain G； PDBConstruct 1–105； UniProt 15–119

Histone H2B

Xenopus laevis

UniProt A0A1L8FQ56

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone deacetylase HDA1 × 1 （P53973） Histone deacetylase HDA1 × 1 （P53973） HDA1 complex subunit 3,HDA1 complex subunit 3 × 1 （Q06623） HDA1 complex subunit 2 × 1 （Q06629） Histone H3 × 1 （A0A310TTQ1） Histone H4 × 1 （P62799） Histone H2A × 1 （Q6AZJ8） Histone H2B × 1 （A0A1L8FQA5） Histone H3.2 × 1 （P84233） Histone H4 × 1 （P62799） Histone H2A type 1 × 1 （P06897） DNA (145-MER) × 1 DNA (145-MER) × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1L8FQ56_XENLA
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain H； PDBConstruct 1–93； UniProt 33–125

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	6z6p
Deposition date deposition_date	2020-05-28
Structure title title	HDAC-PC-Nuc
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.

6z6p__assembly_1__model_1

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

Download this curve (.dat)

6z6p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6z6p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	64.36 Å
Rg (electron density)	64.13 Å
Total Rg	64.35 Å
Atom count	31115
Residues	3428
Excluded volume	536250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6z6p__assembly_1__model_1`	tetradecameric （14）	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 (15)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K
Atom count atom_count	31115

RQVIVPVCMPKIHYSPLKTGLCYDVRMRYHAKIFTSYFEYIDPHPEDPRRIYRIYKILAENGLINDPTLSGVDDLGDLMLKIPVRAATSEEILEVHTKEHLEFIESTEKMSREELLKETEKGDSVYFNNDSYASARLPCGGAIEACKAVVEGRVKNSLAVVRPPGHHAEPQAAGGFCLFSNVAVAAKNILKNYPESVRRIMILDWDIHHGNGTQKSFYQDDQVLYVSLHRFEMGKYYPGTIQGQYDQTGEGKGEGFNCNITWPVGGVGDAEYMWAFEQVVMPMGREFKPDLVIISSGFDAADGDTIGQCHVTPSCYGHMTHMLKSLARGNLCVVLEGGYNLDAIARSALSVAKVLIGEPPDELPDPLSDPKPEVIEMIDKVIRLQSKYWNCFRRRHANSGCNFNEPINDSIISKNFPLQKAIRQQQQHYLSDEFNFVTLPLVSMDLPDNTVLCTPNISESNTIIIVVHDTSDIWAKRNVISGTIDLSSSVIIDNSLDFIKWGLDRKYGIIDVNIPLTLFEPDNYSGMITSQEVLIYLWDNYIKYFPSVAKIAFIGIGDSYSGIVHLLGHRDTRAVTKTVINFLGDKQLKPLVPLVDETLSEWYFKNSLIFSNNSHQCWKENESRKPRKKFGRVLRCDTDGLNNIIEERFEEATDFILDSFE

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

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 3,HDA1 complex subunit 3
Molecular weight formula_weight	63422.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

SGDYWLPTTMSLYQKELTDQIVSLHYSDILRYFETSHYKEDVILESMKTMCLNGSLVATHPYLLIDHYMPKSLITRDVPAHLAENSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSKQKANDFSCTVHLFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYLLQYKRERKGLERYAPIVRLVAINSIDHCRLFFGKKFDKNSREYLENVTAAMVILRDRLGTLPPDLRPIYSQKLHYLVEWLENPTVPWPLPDIYPLKQYTSMDVERSLLTEVHFKKNSSNVNYHLSSGIITHKLIQSMGEVYMDICVQKQELDDYSCLDDLQNDHLKFFSNEDEKIIKEYETVLRTNNENLNRSHELEVENNLKFSQIETLEKDIETLKGSLMAQGETLSKLKDAFVKTDNVQDEIEKEERVSVSRDTEKKYMEQEIKRAVDAIRENEEETHKLNEKQNGLESELKLKFEKSEISTKELNEKIGFLKKELKLENDLNEELVGQLSKTMDNLENLTIPRVRTQ

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 2
Molecular weight formula_weight	71915.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

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 5 Entity 5 polymer

Description description	Histone H3
Molecular weight formula_weight	11431.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Histone H4
Molecular weight formula_weight	9409.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Histone H2A
Molecular weight formula_weight	11294.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

TRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Histone H2B
Molecular weight formula_weight	10607.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	Histone H3.2
Molecular weight formula_weight	11405.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 10 Entity 10 polymer

Description description	Histone H4
Molecular weight formula_weight	8795.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 11 Entity 11 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	11494.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 12 Entity 12 polymer

Description description	Histone H2B
Molecular weight formula_weight	10348.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

TRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli

Entity 13 Entity 13 polymer

Description description	DNA (145-MER)
Molecular weight formula_weight	44520.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

Entity 14 Entity 14 polymer

Description description	DNA (145-MER)
Molecular weight formula_weight	44991.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Entity 15 Entity 15 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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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	4.43 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	41279

HDAC-PC-Nuc

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 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

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

Histone H3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H3.2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2A type 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer