SAXSdb — 6wjv

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

DNA polymerase epsilon catalytic subunit A

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P21951

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon subunit B × 1 （P24482） DNA polymerase epsilon subunit C × 1 （P27344） DNA polymerase epsilon subunit D × 1 （Q04603） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOE_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–2222； UniProt 1–2222

DNA polymerase epsilon subunit B

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P24482

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） DNA polymerase epsilon subunit C × 1 （P27344） DNA polymerase epsilon subunit D × 1 （Q04603） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPB2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 2； PDBConstruct 1–689； UniProt 1–689

DNA polymerase epsilon subunit C

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P27344

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） DNA polymerase epsilon subunit B × 1 （P24482） DNA polymerase epsilon subunit D × 1 （Q04603） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPB3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain 3； PDBConstruct 1–201； UniProt 1–201

DNA polymerase epsilon subunit D

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q04603

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	DNA polymerase epsilon catalytic subunit A × 1 （P21951） DNA polymerase epsilon subunit B × 1 （P24482） DNA polymerase epsilon subunit C × 1 （P27344） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPB4_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain 4； PDBConstruct 1–196； UniProt 1–196

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	6wjv
Deposition date deposition_date	2020-04-14
Structure title title	Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme
Keywords keywords	DNA replication, DNA polymerase, CELL CYCLE; CELL CYCLE
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.

6wjv__assembly_1__model_1

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

Download this curve (.dat)

6wjv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wjv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.01 Å
Rg (electron density)	50.99 Å
Total Rg	51.02 Å
Atom count	19593
Residues	2567
Excluded volume	348830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wjv__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 (5)

Entity 1 Entity 1 polymer

Description description	DNA polymerase epsilon catalytic subunit A
Molecular weight formula_weight	255992.5 kDa
EC 编号 ec_number	2.7.7.7,3.1.11.-
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	19593

MMFGKKKNNGGSSTARYSAGNKYNTLSNNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLTNMHATLVSQETLSSGSNGGGNSNDGERVTTNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFEARKLLRPILQDNANNNVQRNIYNVAANGSEKVDAKHLIEDIREYDVPYHVRVSIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRLQPDSIKAERDCASCDFNRPGKTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKFSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHPDWLKRKIATKEDKFKQTSLTKFFSKTKNVPTMGKIKDIEDLFEPTVEEDNAKIKIARTTKKKAVSKRKRNQLTNEEDPLVLPSEIPSMDEDYVGWLNYQKIKWKIQARDRKRRDQLFGNTNSSRERSALGSMIRKQAESYANSTWEVLQYKDSGEPGVLEVFVTINGKVQNITFHIPKTIYMKFKSQTMPLQKIKNCLIEKSSASLPNNPKTSNPAGGQLFKITLPESVFLEEKENCTSIFNDENVLGVFEGTITPHQRAIMDLGASVTFRSKAMGALGKGIQQGFEMKDLSMAENERYLSGFSMDIGYLLHFPTSIGYEFFSLFKSWGDTITILVLKPSNQAQEINASSLGQIYKQMFEKKKGKIETYSYLVDIKEDINFEFVYFTDISKLYRRLSQETTKLKEERGLQFLLLLQSPFITKLLGTIRLLNQMPIVKLSLNEVLLPQLNWQPTLLKKLVNHVLSSGSWISHLIKLSQYSNIPICNLRLDSMDYIIDVLYARKLKKENIVLWWNEKAPLPDHGGIQNDFDLNTSWIMNDSEFPKINNSGVYDNVVLDVGVDNLTVNTILTSALINDAEGSDLVNNNMGIDDKDAVINSPSEFVHDAFSNDALNVLRGMLKEWWDEALKENSTADLLVNSLASWVQNPNAKLFDGLLRYHVHNLTKKALLQLVNEFSALGSTIVYADRNQILIKTNKYSPENCYAYSQYMMKAVRTNPMFSYLDLNIKRYWDLLIWMDKFNFSGLACIEIEEKENQDYTAVSQWQLKKFLSPIYQPEFEDWMMIILDSMLKTKQSYLKLNSGTQRPTQIVNVKKQDKEDSVENSLNGFSHLFSKPLMKRVKKLFKNQQEFILDPQYEADYVIPVLPGSHLNVKNPLLELVKSLCHVMLLSKSTILEIRTLRKELLKIFELREFAKVAEFKDPSLSLVVPDFLCEYCFFISDIDFCKAAPESIFSCVRCHKAFNQVLLQEHLIQKLRSDIESYLIQDLRCSRCHKVKRDYMSAHCPCAGAWEGTLPRESIVQKLNVFKQVAKYYGFDILLSCIADLTI

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	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	DNA polymerase epsilon subunit B
Molecular weight formula_weight	78425.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

MFGSGNVLPVKIQPPLLRPLAYRVLSRKYGLSIKSDGLSALAEFVGTNIGANWRQGPATIKFLEQFAAVWKQQERGLFIDQSGVKEVIQEMKEREKVEWSHEHPIQHEENILGRTDDDENNSDDEMPIAADSSLQNVSLSSPMRQPTERDEYKQPFKPESSKALDWRDYFKVINASQQQRFSYNPHKMQFIFVPNKKQNGLGGIAGFLPDIEDKVQMFLTRYYLTNDRVMRNENFQNSDMFNPLSSMVSLQNELSNTNRQQQSSSMSITPIKNLLGRDAQNFLLLGLLNKNFKGNWSLEDPSGSVEIDISQTIPTQGHYYVPGCMVLVEGIYYSVGNKFHVTSMTLPPGERREITLETIGNLDLLGIHGISNNNFIARLDKDLKIRLHLLEKELTDHKFVILGANLFLDDLKIMTALSKILQKLNDDPPTLLIWQGSFTSVPVFASMSSRNISSSTQFKNNFDALATLLSRFDNLTENTTMIFIPGPNDLWGSMVSLGASGTLPQDPIPSAFTKKINKVCKNVVWSSNPTRIAYLSQEIVIFRDDLSGRFKRHRLEFPFNESEDVYTENDNMMSKDTDIVPIDELVKEPDQLPQKVQETRKLVKTILDQGHLSPFLDSLRPISWDLDHTLTLCPIPSTMVLCDTTSAQFDLTYNGCKVINPGSFIHNRRARYMEYVPSSKKTIQEEIYI

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	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	DNA polymerase epsilon subunit C
Molecular weight formula_weight	22694.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

MSNLVKEKAPVFPISKVKKIAKCDPEYVITSNVAISATAFAAELFVQNLVEESLVLAQLNSKGKTSLRLSLNSIEECVEKRDNFRFLEDAIKQLKKNSALDKKRELNMQPGRSDQEVVIEEPELHEDDGVEEEEEEDEVSEEEEPVHNEELLDDSKDQQNDKSTRSVASLLSRFQYKSALDVGEHSDSSDIEVDHTKSTDP

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	Saccharomyces cerevisiae

Entity 4 Entity 4 polymer

Description description	DNA polymerase epsilon subunit D
Molecular weight formula_weight	22029.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

MPPKGWRKDAQGNYPTTSYIKEQENITIQDLLFPKSTIVNLAREVPQQSGKKLLINKDASLALQRGATVFVNHLLLFAREIAKSQDKKSCSVDDVLSALDHIGHSALKGPVRDKLDEYQAAVEQRKKEKLDSGEVDADGDIDMGEDKENVPVEKVKEHDEIEEQGDALQDVEESSEKKQKTESQDVETRVQNLEQT

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	Saccharomyces cerevisiae

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	1

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Resolution resolution	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	187298

Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme

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

DNA polymerase epsilon catalytic subunit A

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase epsilon subunit B

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase epsilon subunit C

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase epsilon subunit D

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

6wjv__assembly_1__model_1

6wjv__assembly_1__model_1 | I(q)

6wjv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

7. Citations (1)

Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme

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

DNA polymerase epsilon catalytic subunit A

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 epsilon subunit B

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 epsilon subunit C

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 epsilon subunit 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

6wjv__assembly_1__model_1

6wjv__assembly_1__model_1 | I(q)

6wjv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

7. Citations (1)