6knb

PolD-PCNA-DNA (form A)

Method: ELECTRON MICROSCOPY

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

DNA polymerase II small subunit

Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 5 DNA 2	DNA polymerase D DP2 (DNA polymerase II large) subunit × 1 DNA polymerase sliding clamp 1 × 3 （Q5JF32） pri25DNA × 1 temp35DNA × 1 FE (III) ION × 1 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5JET1_THEKO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 65–537； UniProt 263–735

DNA polymerase sliding clamp 1

Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

UniProt Q5JF32

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 5 DNA 2	DNA polymerase II small subunit × 1 （Q5JET1） DNA polymerase D DP2 (DNA polymerase II large) subunit × 1 pri25DNA × 1 temp35DNA × 1 FE (III) ION × 1 ZINC ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA1_THEKO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–249； UniProt 1–249 Author chain D； PDBConstruct 1–249； UniProt 1–249 Author chain E； PDBConstruct 1–249； UniProt 1–249

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	6knb
Deposition date deposition_date	2019-08-05
Structure title title	PolD-PCNA-DNA (form A)
Keywords keywords	Family D Polymerase, PCNA, Switch Hook, REPLICATION, REPLICATION-DNA complex; REPLICATION/DNA
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.

6knb__assembly_1__model_1

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

Download this curve (.dat)

6knb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6knb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.42 Å
Rg (electron density)	45.06 Å
Total Rg	45.24 Å
Atom count	19581
Residues	2367
Excluded volume	348140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6knb__assembly_1__model_1`	heptameric （7）	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 (7)

Entity 1 Entity 1 polymer

Description description	DNA polymerase II small subunit
Molecular weight formula_weight	60772.3 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	A
Atom count atom_count	19581

MLVEDLLKNNYLITPSAYYLLSDHYKKAFTLAELIKFAKNRGTFVVDSNLAREFLAEKGIISSGIVYGDYGVPIAYVADETPEEEKAYSTYSDLVIAPKEGFHYRAKEIPDEWELAFDVKNVKFEVPKVKNAQSKEGEVIIQAYSSYFKSRLKKMRRIFRENPEIGTIVDIAKLSYVREDDVTIIGLVNEKRETRKGYLFEIEDATGRIKVFIGSDKEGANEAYSTIMPDSVVAFRGTPGKGIFFANRVFLPDVPKFKRSKPPLEEKVYAILLSDIHVGSNKFCEEAFIKFLEWLNGEVNSRTEEELVSRIKYIIIGGDVVDGVGIYPGQYNELAIPDIFDQYEALANLLKQVPDHITMFIGPGNHDAARTALPQPGFYEEYAKPLYKLKNAVIISNPAVIRLHGRDFLVAHGRGIEDVVDFVPNRSHHRPAEAMVELLKLRHIAPTFGNKVPIAPDPEDTLVIESVPDLFQAGHVHVMQYKTYNGVFVINTGTWQAQTEFQKMVNIIPTPARVPIIDVETARLRAVVRFDQFCEGV

Source Source

Source organism organism	Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA polymerase D DP2 (DNA polymerase II large) subunit
Molecular weight formula_weight	150418.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSEEIYSPEMKAYFESLQREIDRAYAIARKARAQGKDPSFDVEVPQATDMAGRVESLVGPPGVAERIRELVKEYGKEIAALKVVDEIIEGKFGDLGSKEKYAEQAVRTALAILTEGIVSAPLEGIADVKIKRNEWADGSEYLALYYAGPIRSSGGTAQALSVLVGDYVRRKLGLDRFKPSDEHIERMVEEVDLYHRAVTRLQYHPEADEVRLAMRNIPIEITGEETDKVEVSHRNVPGVETNHLRGGAILVLAEGVLQKAKKLVKYIDKMGIEGWDWIKEFVEAKEKGKSSEENKDESKAEDTGTESVAEKKENVEKGFYYELYEKFRANIAPNKKYTKEIIGGRPLFAEPSTNGGFRLRYGRSRVSGFATWSVNPATMLILDEFIAIGTQMKTERPGKGCIVTPATTVEGPIVRLKNGSVVRVDDYETALKVRNEVDEILYVGDALVNFGDFVENNQTLLPANYVEEWWVQELVQAIKDLYEVELQPFAENDREAVEEAAEYLEVDPDFLWNLLKDPLRVKPDVETAIHLSTVLDIPFHPYYTLYWNTLQPEEVEELQKALLGAQIEWAEFRKNRFAKKVVLENDKNIKRYLELLGLPHRLERVEKKRKVIVVEYPWSAALLTPLGNLEWEFKAKPFYTVIDIINENNRIKLRDRGISWIGARMGRPEKAKERKMKPPVQVLFPIGLAGGQSRDIKKAAEEGKTARVEIAFFKCPKCGHVGPEHLCPVCGTRKELLWHCPKCGADYPESDAKDFNYRCPKCDVELKPYAEREIKPADLLRQAMDNVKVYGIDRLKGVKGMTSGYKMAEPLEKGLLRVKNDVYVFKDGTIRFDATDAPITHFKPKEIGTSVEKLRELGYTHDFEGKPLERDDQILELKVQDVILPYEAGRYLLKVARFIDDLLEKFYGLPRFYNAEKMEDLVGHLVIGLAPHTSAGIIGRIIGFSDVLVGYAHPYYHAAKRRNCDGDEDAVMLLLDALLNFSKYYLPEKRGGKMDAPLVVTTRLDPREVDSEVHNMDVVRYYPLEFYKATYELKSPKEVKVIERVEDRLGKPEMYEGIKFTHDTDDIGLGPKMSLYKQLGDMEEKVARQLALAERIRAVDEHHVAETIINSHLVPDLRGNLRSFTRQEFRCVKCNTKYRRPPLTGKCPKCGGKIVLTVSKGAIEKYLPTAKMLVTKYRVKDYTRQRICITEKDIKTLFENVFPEKQRTLMGFSADICEKMVKERTGHSNGKNGYLDEFNGKNGKASKKSGSLASKLSGKGKEPSKKKESAKPKRSEKVKNLTSFEAAAKNEQARGTAGNAKKAESEKPKRKKRKGISLDEFFGS

Source Source

Source organism organism	Thermococcus kodakarensis
NCBI taxonomy ID ncbi_taxonomy_id	311400
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	DNA polymerase sliding clamp 1
Molecular weight formula_weight	28270.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MPFEVVFDGAKEFADLIATASNLIDEAAFKFTEEGISMRAMDPSRVVLIDLNLPESIFSKYEVEEPETIGINMDQFKKILKRGKAKDTLILRKGDENFLEITFEGTAKRTFRLPLIDVEELELELPELPFTAKVVLLGEVLKEGIKDASLVSDAIKFIAKENEFTMKAEGETNEVEIRLTLEDEGLLDLEVEEETKSAYGIRYLSDMVKGIGKADEVILRFGNEMPLQMEYMIRDEGRLTFLLAPRVEE

Source Source

Source organism organism	Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	pri25DNA
Molecular weight formula_weight	9233.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

CGAACTGCCTGGAATCCTGACGACATGTAG

Entity 5 Entity 5 polymer

Description description	temp35DNA
Molecular weight formula_weight	9214.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CTACATGTCGTCAGGATTCCAGGCAGTTCG

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

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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	6.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	41073

PolD-PCNA-DNA (form A)

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 sliding clamp 1

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

6knb__assembly_1__model_1

6knb__assembly_1__model_1 | I(q)

6knb__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 (7)

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 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

PolD-PCNA-DNA (form A)

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 sliding clamp 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

6knb__assembly_1__model_1

6knb__assembly_1__model_1 | I(q)

6knb__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 (7)

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 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)