SAXSdb — 6nq3

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

Histone-binding protein RBBP4

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Polycomb protein SUZ12 × 2 （Q15022） PHD finger protein 19 × 2 （Q5T6S3） Protein Jumonji × 2 （Q92833） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Polycomb protein SUZ12 × 2 （Q15022） PHD finger protein 19 × 2 （Q5T6S3） Protein Jumonji × 2 （Q92833） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBBP4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–439； UniProt 1–425 Author chain E； PDBConstruct 15–439； UniProt 1–425

Polycomb protein SUZ12

Homo sapiens

UniProt Q15022

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Histone-binding protein RBBP4 × 2 （Q09028） PHD finger protein 19 × 2 （Q5T6S3） Protein Jumonji × 2 （Q92833） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Histone-binding protein RBBP4 × 2 （Q09028） PHD finger protein 19 × 2 （Q5T6S3） Protein Jumonji × 2 （Q92833） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SUZ12_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–470； UniProt 76–545 Author chain F； PDBConstruct 1–470； UniProt 76–545

PHD finger protein 19

Homo sapiens

UniProt Q5T6S3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Histone-binding protein RBBP4 × 2 （Q09028） Polycomb protein SUZ12 × 2 （Q15022） Protein Jumonji × 2 （Q92833） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Histone-binding protein RBBP4 × 2 （Q09028） Polycomb protein SUZ12 × 2 （Q15022） Protein Jumonji × 2 （Q92833） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHF19_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–84； UniProt 500–580 Author chain G； PDBConstruct 4–84； UniProt 500–580

Protein Jumonji

OrganismNot specified

UniProt Q92833

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Histone-binding protein RBBP4 × 2 （Q09028） Polycomb protein SUZ12 × 2 （Q15022） PHD finger protein 19 × 2 （Q5T6S3） ZINC ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Histone-binding protein RBBP4 × 2 （Q09028） Polycomb protein SUZ12 × 2 （Q15022） PHD finger protein 19 × 2 （Q5T6S3） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	JARD2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–19； UniProt 147–165 Author chain H； PDBConstruct 1–19； UniProt 147–165

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	6nq3
Deposition date deposition_date	2019-01-19
Structure title title	Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex
Keywords keywords	Methyltransferase, TRANSCRIPTION; TRANSCRIPTION
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.

6nq3__assembly_1__model_1

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

Download this curve (.dat)

6nq3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nq3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.90 Å
Rg (electron density)	40.62 Å
Total Rg	41.01 Å
Atom count	12044
Residues	1484
Excluded volume	213670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nq3__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nq3__assembly_2__model_1`	octameric （8）	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-binding protein RBBP4
Molecular weight formula_weight	49367.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	11928

MSHHHHHHLVPRGSMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDPEGQGS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Polycomb protein SUZ12
Molecular weight formula_weight	55686.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MEHVQADHELFLQAFEKPTQIYRFLRTRNLIAPIFLHRTLTYMSHRNSRTNIKRKTFKVDDMLSKVEKMKGEQESHSLSAHLQLTFTGFFHKNDKPSPNSENEQNSVTLEVLLVKVCHKKRKDVSCPIRQVPTGKKQVPLNPDLNQTKPGNFPSLAVSSNEFEPSNSHMVKSYSLLFRVTRPGRREFNGMINGETNENIDVNEELPARRKRNREDGEKTFVAQMTVFDKNRRLQLLDGEYEVAMQEMEECPISKKRATWETILDGKRLPPFETFSQGPTLQFTLRWTGETNDKSTAPIAKPLATRNSESLHQENKPGSVKPTQTIAVKESLTTDLQTRKEKDTPNENRQKLRIFYQFLYNNNTRQQTEARDDLHCPWCTLNCRKLYSLLKHLKLCHSRFIFNYVYHPKGARIDVSINECYDGSYAGNPQDIHRQPGFAFSRNGPVKRTPITHILVCRPKRTKASMSEFLEWSHPQFEK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	PHD finger protein 19
Molecular weight formula_weight	9092.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SNASDSSAEGASVPERPDEGIDSHTFESISEDDSSLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLVEWEGTTPY

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 4 Entity 4 polymer

Description description	Protein Jumonji
Molecular weight formula_weight	2257.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

LSKRKPKTEDFLTFLCLRG

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	2

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6nq3A00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	6nq3E00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	127.710 Å
Unit-cell length b length_b	139.600 Å
Unit-cell length c length_c	268.080 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	46.600 Å
R factor r_factor	0.1730
R_work r_work	0.1700
R_free r_free	0.2300

Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex

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

Histone-binding protein RBBP4

State in the Current Structure

Other States of the Same Protein in the Database

Polycomb protein SUZ12

State in the Current Structure

Other States of the Same Protein in the Database

PHD finger protein 19

State in the Current Structure

Other States of the Same Protein in the Database

Protein Jumonji

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

6nq3__assembly_1__model_1

6nq3__assembly_1__model_1 | I(q)

6nq3__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 (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

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex

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

Histone-binding protein RBBP4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polycomb protein SUZ12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHD finger protein 19

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein Jumonji

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

6nq3__assembly_1__model_1

6nq3__assembly_1__model_1 | I(q)

6nq3__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 (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

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)