SAXSdb — 9f2a

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

DNA polymerase II small subunit

Pyrococcus abyssi GE5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase II large subunit × 1 （P81409） RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination × 1 （Q9V1Z1） FE (III) ION × 1 ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DP2S_PYRAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 45–662； UniProt 2–619

DNA polymerase II large subunit

Pyrococcus abyssi GE5

UniProt P81409

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase II small subunit × 1 （Q9V2F3） RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination × 1 （Q9V1Z1） FE (III) ION × 1 ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DP2L_PYRFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1268； UniProt 1–1263

RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination

Pyrococcus abyssi GE5

UniProt Q9V1Z1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA polymerase II small subunit × 1 （Q9V2F3） DNA polymerase II large subunit × 1 （P81409） FE (III) ION × 1 ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9V1Z1_PYRAB
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 42–132； UniProt 182–272

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	9f2a
Deposition date deposition_date	2024-04-22
Structure title title	Pyrococcus abyssi PolD in complex with Rpa2 winged-helix domain class 2 (composite map)
Keywords keywords	DNA Polymerase, Archaea, replication, RPA; REPLICATION
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.

9f2a__assembly_1__model_1

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

Download this curve (.dat)

9f2a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9f2a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.07 Å
Rg (electron density)	42.88 Å
Total Rg	43.12 Å
Atom count	13557
Residues	1692
Excluded volume	243720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9f2a__assembly_1__model_1`	trimeric （3）	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	DNA polymerase II small subunit
Molecular weight formula_weight	74009.7 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	13557

MGKHHHHSGHHHTGHHHHSGSHHHTSSSASTGENLYFQGTGDGSDELVKALERAGYLLTPSAYYLLVDHFKEGKFSLVELVKFAKSKGVFIIDGDLAYEFLQFLGLGVPQEIKESYISTGEEAEKTVESQETRASELEEGGVSQVSSGELQELKEESPEISTTEEEIGGLELVQSSISTGSEVEYNNGENGESVVVLDKYGYPILYAPEEIGEEKEYSKYEDVVIEWNPSVTPVQIEKNYEVKFDVRQVKLRPPKVKNGSGKEGEIIVEAYASLFKSRLSKLKRILRENPEISNVVDIGKLNYVSGDEEVTIIGLVNSKRETNRGLIFEVEDKTGIVKVFLPKDSEDYREAFKVLPDAVVAFKGFYSKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKAFLKFLEWLNGHVESKEEEEIVSRVKYLIIAGDVVDGIGIYPGQYSDLVIPDIFDQYEALANLLANVPEHITMFIGPGNADAARPAIPQPEFYKEYAKPIYKLKNAIIISNPAVIRLHGRDFLIAHGRGIEDVVSFVPGLTHHKPGLPMVELLKMRHLAPTFGGKVPIAPDPEDLLVIEEVPDLVQMGHVHVYDAVVYRGVQLVNSATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC

Source Source

Source organism organism	Pyrococcus abyssi GE5
NCBI taxonomy ID ncbi_taxonomy_id	272844
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA polymerase II large subunit
Molecular weight formula_weight	144419.0 kDa
EC 编号 ec_number	2.7.7.7,3.1.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MELPKEMEEYFEMLQREIDKAYEIAKKARAQGKDPSLDVEIPQATDMAGRVESLVGPPGVAKRIRELVKEYGKEIAALKIVDEIIEGKFGDLGSREKYAEQAVRTALAILTEGIVSAPIEGIANVKIKRNTWADNSEYLALYYAGPIRSSGGTAQALSVLVGDYVRRKLGLDRFKPSEKHIERMVEEVDLYHRAVTRLQYHPSPEEVRLAMRNIPIEITGEATDDVEVSHRDVPGVETNQLRGGAILVLAEGVLQKAKKLVKYIDKMGIEGWEWLKEFVEAKEKGEPKEEGKEESLAESTLEETKVEVDMGFYYSLYQKFKEEIAPSDKYAKEVIGGRPLFSDPSKPGGFRLRYGRSRASGFATWGINPATMILVDEFLAIGTQLKTERPGKGAVVTPVTTIEGPIVKLKDGSVLRVDDYNLALKVREDVEEILYLGDAVIAFGDFVENNQTLLPANYCEEWWILEFVKALKEIYEVHLEPFTENEEESIEEASDYLEIDPEFLKEMLRDPLRVKPPVELAIHFSEVLGIPLHPYYTLYWNSVEPKDVEKLWRLLKNYAEIEWSNFRGIKFAKKIVISQEKLGDSKRTLELLGLPHTVRDGNVIVDYPWAAALLTPLGNLNWEFMAKPLYATIDIINENNEIKLRDRGISWIGARMGRPEKAKERKMKPPVQVLFPIGLAGGSSRDIKKAAEEGKVAEVEIAFFKCPKCGHVGPEHLCPNCGTRKELLWVCPRCNAEYPESQAEGYNYTCPKCNVKLRPYAKRKIRPSELLNRAMENVKVYGVDKLKGVMGMTSGWKMPEPLEKGLLRAKNDVYVFKDGTIRFDATDAPITHFRPREIGVSVEKLRELGYTHDFEGKPLVSEDQIVELKPQDIILSKEAGRYLLKVAKFVDDLLEKFYGLPRFYNAEKMEDLIGHLVIGLAPHTSAGIVGRIIGFVDALVGYAHPYFHAAKRRNCDGDEDAVMLLLDALLNFSRYYLPEKRGGKMDAPLVITTRLDPREVDSEVHNMDIVRYYPLEFYEATYELKSPKELVGVIERVEDRLGKPEMYYGLKFTHDTDDIALGPKMSLYKQLGDMEEKVRRQLEVAKRIRAVDEHGVAEKILNSHLIPDLRGNLRSFTRQEFRCVKCNTKFRRPPLNGKCPVCGGKIVLTVSKGAIEKYLGTAKMLVTEYNVKNYTRQRICLTERDIDSLFENVFPETQLTLIVNPNDICQRLVMARTGEVNKSGLLENLSNGSKKTEKAEKAEKPRKKSDEKPKKKRVISLEEFFSRKSK

Source Source

Source organism organism	Pyrococcus abyssi GE5
NCBI taxonomy ID ncbi_taxonomy_id	272844
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination
Molecular weight formula_weight	15264.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGKHHHHSGHHHTGHHHHSGSHHHTSSSASTGENLYFQGTGGIMMEERSIEEPMEELLEEEIPEEKEENELLEKAKEDILNILRQKRTAISRKYILKKLGDKYDEETIDDAITELLAQGEIYEPETGYYKLL

Source Source

Source organism organism	Pyrococcus abyssi GE5
NCBI taxonomy ID ncbi_taxonomy_id	272844
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

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	3

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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	—

Resolution resolution	2.91 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	174709

Pyrococcus abyssi PolD in complex with Rpa2 winged-helix domain class 2 (composite map)

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

DNA polymerase II small subunit

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase II large subunit

State in the Current Structure

Other States of the Same Protein in the Database

RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination

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

9f2a__assembly_1__model_1

9f2a__assembly_1__model_1 | I(q)

9f2a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Pyrococcus abyssi PolD in complex with Rpa2 winged-helix domain class 2 (composite map)

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

DNA polymerase II small subunit

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 polymerase II large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RPA32 subunit of the hetero-oligomeric complex involved in homologous recombination

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

9f2a__assembly_1__model_1

9f2a__assembly_1__model_1 | I(q)

9f2a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)