6vyp

Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate

Method: X-RAY DIFFRACTION

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

Histone H3

Xenopus laevis

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 H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136 Author chain a； PDBConstruct 1–135； UniProt 2–136 Author chain e； PDBConstruct 1–135； UniProt 2–136

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 H3 × 2 （A0A310TTQ1） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 2–103 Author chain F； PDBConstruct 1–102； UniProt 2–103 Author chain b； PDBConstruct 1–102； UniProt 2–103 Author chain f； PDBConstruct 1–102； UniProt 2–103

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 H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–129； UniProt 2–130 Author chain G； PDBConstruct 1–129； UniProt 2–130 Author chain c； PDBConstruct 1–129； UniProt 2–130 Author chain g； PDBConstruct 1–129； UniProt 2–130

Histone H2B 1.1

Xenopus laevis

UniProt P02281

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 H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B11_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–122； UniProt 5–126 Author chain H； PDBConstruct 1–122； UniProt 5–126 Author chain d； PDBConstruct 1–122； UniProt 5–126 Author chain h； PDBConstruct 1–122； UniProt 5–126

Lysine-specific histone demethylase 1A

Homo sapiens

UniProt O60341

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 H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 REST corepressor 1 × 2 （Q9UKL0） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDM1A_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 3–684； UniProt 171–852 Author chain M； PDBConstruct 3–684； UniProt 171–852 Author chain k； PDBConstruct 3–684； UniProt 171–852 Author chain m； PDBConstruct 3–684； UniProt 171–852

REST corepressor 1

Homo sapiens

UniProt Q9UKL0

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 H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 12 DNA 2	Histone H3 × 2 （A0A310TTQ1） Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (191-MER) × 1 DNA (191-MER) × 1 Lysine-specific histone demethylase 1A × 2 （O60341） FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RCOR1_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain L； PDBConstruct 3–157； UniProt 289–443 Author chain N； PDBConstruct 3–157； UniProt 289–443 Author chain l； PDBConstruct 3–157； UniProt 289–443 Author chain n； PDBConstruct 3–157； UniProt 289–443

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	6vyp
Deposition date deposition_date	2020-02-27
Structure title title	Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate
Keywords keywords	epigenetics, histone modifications, histone demethylation, NUCLEAR PROTEIN, NUCLEAR PROTEIN-DNA complex; NUCLEAR PROTEIN/DNA
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.

6vyp__assembly_1__model_1

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

Download this curve (.dat)

6vyp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6vyp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	64.46 Å
Rg (electron density)	65.26 Å
Total Rg	65.19 Å
Atom count	26597
Residues	2752
Excluded volume	449250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6vyp__assembly_1__model_1`	tetradecameric （14）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6vyp__assembly_2__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 (9)

Entity 1 Entity 1 polymer

Description description	Histone H3
Molecular weight formula_weight	15305.9 kDa
Mutation mutation	K4M
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,a,e
Atom count atom_count	52996

ARTMQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11263.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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 3 Entity 3 polymer

Description description	Histone H2A type 1
Molecular weight formula_weight	13978.2 kDa
Mutation mutation	G99R/A123S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

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 4 Entity 4 polymer

Description description	Histone H2B 1.1
Molecular weight formula_weight	13524.8 kDa
Mutation mutation	S32T
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

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 5 Entity 5 polymer

Description description	DNA (191-MER)
Molecular weight formula_weight	58694.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,i

ATCGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTATTGAACAGCGACGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	DNA (191-MER)
Molecular weight formula_weight	59245.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,j

ATCGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGCGTATAGGGTCGAT

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Lysine-specific histone demethylase 1A
Molecular weight formula_weight	75732.6 kDa
EC 编号 ec_number	1.-.-.-
Mutation mutation	R608A/N717A/D721A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,m,K,k

GSPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTASTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMEAISDAVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQATPGVPAQQSPSM

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

Entity 8 Entity 8 polymer

Description description	REST corepressor 1
Molecular weight formula_weight	17956.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,n,L,l

GSPTETVPQVKKEKHSTQAKNRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE

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

Entity 9 Entity 9 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

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Unit-cell length a length_a	103.771 Å
Unit-cell length b length_b	335.770 Å
Unit-cell length c length_c	174.633 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.07 °
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	4.990 Å
Low-resolution limit resolution_low	20.170 Å
R factor r_factor	0.2309
R_work r_work	0.2291
R_free r_free	0.2774

Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate

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

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 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 1.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lysine-specific histone demethylase 1A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

REST corepressor 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6vyp__assembly_1__model_1

6vyp__assembly_1__model_1 | I(q)

6vyp__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer