SAXSdb — 8yjf

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

FACT complex subunit SPT16

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	DNA replication licensing factor MCM2 × 1 （P49736） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2B type 2-E × 1 （Q16778） Histone H2A type 1-D × 1 （P20671）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SP16H_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–350； UniProt 644–988

DNA replication licensing factor MCM2

Homo sapiens

UniProt P49736

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	FACT complex subunit SPT16 × 1 （Q9Y5B9） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2B type 2-E × 1 （Q16778） Histone H2A type 1-D × 1 （P20671）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCM2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–93； UniProt 63–154

Histone H3.1

Homo sapiens

UniProt P68431

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	FACT complex subunit SPT16 × 1 （Q9Y5B9） DNA replication licensing factor MCM2 × 1 （P49736） Histone H4 × 2 （P62805） Histone H2B type 2-E × 1 （Q16778） Histone H2A type 1-D × 1 （P20671）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H31_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–81； UniProt 57–136 Author chain E； PDBConstruct 2–81； UniProt 57–136

Histone H4

Homo sapiens

UniProt P62805

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	FACT complex subunit SPT16 × 1 （Q9Y5B9） DNA replication licensing factor MCM2 × 1 （P49736） Histone H3.1 × 2 （P68431） Histone H2B type 2-E × 1 （Q16778） Histone H2A type 1-D × 1 （P20671）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–103； UniProt 1–103 Author chain F； PDBConstruct 1–103； UniProt 1–103

Histone H2B type 2-E

Homo sapiens

UniProt Q16778

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	FACT complex subunit SPT16 × 1 （Q9Y5B9） DNA replication licensing factor MCM2 × 1 （P49736） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-D × 1 （P20671）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B2E_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain G； PDBConstruct 1–126； UniProt 1–126

Histone H2A type 1-D

Homo sapiens

UniProt P20671

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	FACT complex subunit SPT16 × 1 （Q9Y5B9） DNA replication licensing factor MCM2 × 1 （P49736） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2B type 2-E × 1 （Q16778）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A1D_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain H； PDBConstruct 8–136； UniProt 2–130

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	8yjf
Deposition date deposition_date	2024-03-01
Structure title title	Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer
Keywords keywords	DNA replication, histone chaperone, FACT, MCM2, parental histones transfer, REPLICATION; REPLICATION
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.

8yjf__assembly_1__model_1

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

Download this curve (.dat)

8yjf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yjf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.15 Å
Rg (electron density)	31.15 Å
Total Rg	31.84 Å
Atom count	6797
Residues	846
Excluded volume	121030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yjf__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	FACT complex subunit SPT16
Molecular weight formula_weight	40250.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6797

GPLGSGIVKQDSLVINLNRSNPKLKDLYIRPNIAQKRMQGSLEAHVNGFRFTSVRGDKVDILYNNIKHALFQPCDGEMIIVLHFHLKNAIMFGKKRHTDVQFYTEVGEITTDLGKHQHMHDRDDLYAEQMEREMRHKLKTAFKNFIEKVEALTKEELEFEVPFRDLGFNGAPYRSTCLLQPTSSALVNATEWPPFVVTLDEVELIHFERVQFHLKNFDMVIVYKDYSKKVTMINAIPVASLDPIKEWLNSCDLKYTEGVQSLNWTKIMKTIVDDPEGFFEQGGWSFLEPEGEGSDAEEGDSESEIEDETFNPSEDDYEEEEEDSDEDYSSEAEESDYSKESLGSEEESGK

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA replication licensing factor MCM2
Molecular weight formula_weight	10787.6 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQRDREAGRGLGRMRRGLLYDSDEEDEERPARKRRQV

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Histone H3.1
Molecular weight formula_weight	9379.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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 BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Histone H4
Molecular weight formula_weight	11394.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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 BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Histone H2B type 2-E
Molecular weight formula_weight	13951.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

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 BL21(DE3)

Entity 6 Entity 6 polymer

Description description	Histone H2A type 1-D
Molecular weight formula_weight	14838.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MVMKDLLSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

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 BL21(DE3)

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Unit-cell length a length_a	190.405 Å
Unit-cell length b length_b	190.405 Å
Unit-cell length c length_c	79.832 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	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	hexagonal

Resolution resolution	4.400 Å
Low-resolution limit resolution_low	49.130 Å
R factor r_factor	0.3571
R_work r_work	0.2929
R_free r_free	0.3122

Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer

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

FACT complex subunit SPT16

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA replication licensing factor MCM2

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 H3.1

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 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 H2B type 2-E

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-D

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

8yjf__assembly_1__model_1

8yjf__assembly_1__model_1 | I(q)

8yjf__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 (6)

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

7. Citations (1)