SAXSdb — 5zba

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

DNA damage response protein Rtt109, putative

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone chaperone asf1 × 1 （Q4WXX5） Histone H3 × 1 （P61830） Histone H4 × 1 （P02309） COENZYME A × 1 IODIDE ION × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4WUS9_ASPFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–544； UniProt 1–543

Histone chaperone asf1

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)

UniProt Q4WXX5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA damage response protein Rtt109, putative × 1 （Q4WUS9） Histone H3 × 1 （P61830） Histone H4 × 1 （P02309） COENZYME A × 1 IODIDE ION × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASF1_ASPFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 35–188； UniProt 1–154

Histone H3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P61830

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA damage response protein Rtt109, putative × 1 （Q4WUS9） Histone chaperone asf1 × 1 （Q4WXX5） Histone H4 × 1 （P02309） COENZYME A × 1 IODIDE ION × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–136； UniProt 1–136

Histone H4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P02309

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA damage response protein Rtt109, putative × 1 （Q4WUS9） Histone chaperone asf1 × 1 （Q4WXX5） Histone H3 × 1 （P61830） COENZYME A × 1 IODIDE ION × 37	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–103； UniProt 1–103

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	5zba
Deposition date deposition_date	2018-02-10
Structure title title	Crystal structure of Rtt109-Asf1-H3-H4-CoA complex
Keywords keywords	;Histone, acetylation, chaperone, DNA replication, nucleosome assembly, DNA damage, TRANSFERASE, TRANSFERASE-STRUCTURAL PROTEIN complex ;; TRANSFERASE/STRUCTURAL PROTEIN
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.

5zba__assembly_1__model_1

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

Download this curve (.dat)

5zba__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5zba__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.72 Å
Rg (electron density)	26.90 Å
Total Rg	27.43 Å
Atom count	5534
Residues	687
Excluded volume	99375 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5zba__assembly_1__model_1`	tetrameric （4）	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	DNA damage response protein Rtt109, putative
Molecular weight formula_weight	59684.9 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	5534

SMSKVDVDLGDSLAKVLPTGVKVTIRHISSAPSPCVALFAAPPGEEPESTFCENHFLAVSISPNENEESEVIIFGIEVLVYGTAHLTTIFVSKADSTGYLHLLKNAPKVSLLRLISNAFLSFLVQTHQRPGVRLMVSLFARAQNQYLFPGSIENPEKHVLDDRGLIKWWCRVIDPILREYEPETGSHEKAVDDQTQESAKSSATAFLIVPGCDKFETRGFFPITARSDGKDRPRWLNSYPLHQLCDNPNAPPRCLVPRFPDDPKTRFLIDLDDELPESTGAAGSKENSGHWRSVKSLAQFWEMMSFRQECSAGRLVGFLWLVINPPGLVNSVQMTSSRVASRDVENVLSESAKTTHDATKQKDEAASVSSPPHPSTSGLQTSPIALPGVSSSDTHATVQQATGPSAFFWPDTGRGHAVLSEEDYKAAINFLIDQDFNTKHKAIASTKAWAEKVASLADQLWVGQRVEGRNATTEPGQKHTDATTVINTAFVRKRKTADEESDKPGEVRGAPGDSEEVNPTPVQSNQAPSVNVLNANLLRKKKKT

Source Source

Source organism organism	Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
Common name common_name	Aspergillus fumigatus
NCBI taxonomy ID ncbi_taxonomy_id	330879
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Histone chaperone asf1
Molecular weight formula_weight	21098.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSVVSLLGVKIVNNPAPFLAPYQFEITFECLEQLQKDLEWKLTYVGSATSSEYDQELDSLLVGPIPVGVNKFLFEADAPDLKRIPTSEILGVTVILLTCSYDGREFVRVGYYVNNEYDSEELTQDPPAKPIIERIRRNILAEKPRVTRFAIKWD

Source Source

Source organism organism	Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
Common name common_name	Aspergillus fumigatus
NCBI taxonomy ID ncbi_taxonomy_id	330879
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Histone H3
Molecular weight formula_weight	15391.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTIQKKDIKLARRLRGERS

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 polymer

Description description	Histone H4
Molecular weight formula_weight	11395.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21

Entity 5 Entity 5 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	37

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5zbaB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1490 — Histone chaperone ASF1-like

Domain ID domain_id	5zbaC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5zbaD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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Unit-cell length a length_a	111.903 Å
Unit-cell length b length_b	111.903 Å
Unit-cell length c length_c	332.715 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 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	42.825 Å
R factor r_factor	0.2454
R_work r_work	0.2429
R_free r_free	0.2945

Crystal structure of Rtt109-Asf1-H3-H4-CoA complex

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

DNA damage response protein Rtt109, putative

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 chaperone asf1

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5zba__assembly_1__model_1

5zba__assembly_1__model_1 | I(q)

5zba__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 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)