8dqz

Intermediate state of RFC:PCNA bound to a 3' ss/dsDNA junction

Method: ELECTRON MICROSCOPY

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

Replication factor C subunit 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Replication factor C subunit 4 × 1 （P40339） Replication factor C subunit 3 × 1 （P38629） Replication factor C subunit 2 × 1 （P40348） Replication factor C subunit 5 × 1 （P38251） Proliferating cell nuclear antigen × 3 （P15873） ;DNA (5'-D(PTPTPTPTPTPTPCPGPGPGPGPGPGPGPCPCPCPCPGPGPGPG)-3') ; × 1 ;DNA (5'-D(PCPCPCPCPGPGPGPGPCPCPCPCPCPCPCPGPGPC)-3') ; × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 4 GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFC1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–861； UniProt 1–861

Replication factor C subunit 4

Saccharomyces cerevisiae

UniProt P40339

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Replication factor C subunit 1 × 1 （P38630） Replication factor C subunit 3 × 1 （P38629） Replication factor C subunit 2 × 1 （P40348） Replication factor C subunit 5 × 1 （P38251） Proliferating cell nuclear antigen × 3 （P15873） ;DNA (5'-D(PTPTPTPTPTPTPCPGPGPGPGPGPGPGPCPCPCPCPGPGPGPG)-3') ; × 1 ;DNA (5'-D(PCPCPCPCPGPGPGPGPCPCPCPCPCPCPCPGPGPC)-3') ; × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 4 GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFC4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–323； UniProt 1–323

Replication factor C subunit 3

Saccharomyces cerevisiae

UniProt P38629

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Replication factor C subunit 1 × 1 （P38630） Replication factor C subunit 4 × 1 （P40339） Replication factor C subunit 2 × 1 （P40348） Replication factor C subunit 5 × 1 （P38251） Proliferating cell nuclear antigen × 3 （P15873） ;DNA (5'-D(PTPTPTPTPTPTPCPGPGPGPGPGPGPGPCPCPCPCPGPGPGPG)-3') ; × 1 ;DNA (5'-D(PCPCPCPCPGPGPGPGPCPCPCPCPCPCPCPGPGPC)-3') ; × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 4 GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFC3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–340； UniProt 1–340

Replication factor C subunit 2

Saccharomyces cerevisiae

UniProt P40348

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Replication factor C subunit 1 × 1 （P38630） Replication factor C subunit 4 × 1 （P40339） Replication factor C subunit 3 × 1 （P38629） Replication factor C subunit 5 × 1 （P38251） Proliferating cell nuclear antigen × 3 （P15873） ;DNA (5'-D(PTPTPTPTPTPTPCPGPGPGPGPGPGPGPCPCPCPCPGPGPGPG)-3') ; × 1 ;DNA (5'-D(PCPCPCPCPGPGPGPGPCPCPCPCPCPCPCPGPGPC)-3') ; × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 4 GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFC2_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–353； UniProt 1–353

Replication factor C subunit 5

Saccharomyces cerevisiae

UniProt P38251

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Replication factor C subunit 1 × 1 （P38630） Replication factor C subunit 4 × 1 （P40339） Replication factor C subunit 3 × 1 （P38629） Replication factor C subunit 2 × 1 （P40348） Proliferating cell nuclear antigen × 3 （P15873） ;DNA (5'-D(PTPTPTPTPTPTPCPGPGPGPGPGPGPGPCPCPCPCPGPGPGPG)-3') ; × 1 ;DNA (5'-D(PCPCPCPCPGPGPGPGPCPCPCPCPCPCPCPGPGPC)-3') ; × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 4 GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFC5_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–354； UniProt 1–354

Proliferating cell nuclear antigen

Saccharomyces cerevisiae

UniProt P15873

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Replication factor C subunit 1 × 1 （P38630） Replication factor C subunit 4 × 1 （P40339） Replication factor C subunit 3 × 1 （P38629） Replication factor C subunit 2 × 1 （P40348） Replication factor C subunit 5 × 1 （P38251） ;DNA (5'-D(PTPTPTPTPTPTPCPGPGPGPGPGPGPGPCPCPCPCPGPGPGPG)-3') ; × 1 ;DNA (5'-D(PCPCPCPCPGPGPGPGPCPCPCPCPCPCPCPGPGPC)-3') ; × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 MAGNESIUM ION × 4 GUANOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 20–277； UniProt 1–258 Author chain G； PDBConstruct 20–277； UniProt 1–258 Author chain H； PDBConstruct 20–277； UniProt 1–258

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	8dqz
Deposition date deposition_date	2022-07-20
Structure title title	Intermediate state of RFC:PCNA bound to a 3' ss/dsDNA junction
Keywords keywords	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.

8dqz__assembly_1__model_1

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

Download this curve (.dat)

8dqz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dqz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.26 Å
Rg (electron density)	42.97 Å
Total Rg	43.25 Å
Atom count	42822
Residues	2639
Excluded volume	381530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dqz__assembly_1__model_1`	decameric （10）	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 (11)

Entity 1 Entity 1 polymer

Description description	Replication factor C subunit 1
Molecular weight formula_weight	101689.1 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	42822

MVNISDFFGKNKKSVRSSTSRPTRQVGSSKPEVIDLDTESDQESTNKTPKKMPVSNVIDVSETPEGEKKLPLPAKRKASSPTVKPASSKKTKPSSKSSDSASNITAQDVLDKIPSLDLSNVHVKENAKFDFKSANSNADPDEIVSEIGSFPEGKPNCLLGLTIVFTGVLPTLERGASEALAKRYGARVTKSISSKTSVVVLGDEAGPKKLEKIKQLKIKAIDEEGFKQLIAGMPAEGGDGEAAEKARRKLEEQHNIATKEAELLVKKEEERSKKLAATRVSGGHLERDNVVREEDKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQVINLLSTISTTTKTINHENINEISKAWEKNIALKPFDIAHKMLDGQIYSDIGSRNFTLNDKIALYFDDFDFTPLMIQENYLSTRPSVLKPGQSHLEAVAEAANCISLGDIVEKKIRSSEQLWSLLPLHAVLSSVYPASKVAGHMAGRINFTAWLGQNSKSAKYYRLLQEIHYHTRLGTSTDKIGLRLDYLPTFRKRLLDPFLKQGADAISSVIEVMDDYYLTKEDWDSIMEFFVGPDVTTAIIKKIPATVKSGFTRKYNSMTHPVAIYRTGSTIGGGGVGTSTSTPDFEDVVDADDNPVPADDEETQDSSTDLKKDKLIKQKAKPTKRKTATSKPGGSKKRKTKAGLNENLYFQGGGDYKDDDDKDYKDDDDKDYKDDDDKGGKDHLIHNVHKEEHAHAHNK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Replication factor C subunit 4
Molecular weight formula_weight	36201.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSKTLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKMLLASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIHKLNNKA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	Replication factor C subunit 3
Molecular weight formula_weight	38254.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSTSTEKRSKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQGSAVIGAIKASFENETVKANV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 4 Entity 4 polymer

Description description	Replication factor C subunit 2
Molecular weight formula_weight	39794.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MFEGFGPNKKRKISKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 5 Entity 5 polymer

Description description	Replication factor C subunit 5
Molecular weight formula_weight	39993.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 6 Entity 6 polymer

Description description	Proliferating cell nuclear antigen
Molecular weight formula_weight	30991.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,H

MGSSHHHHHHSSGLVPRASMLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Saccharomyces cerevisiae

Entity 7 Entity 7 polymer

Description description	;DNA (5'-D(PTPTPTPTPTPTPCPGPGPGPGPGPGPGPCPCPCPCPGPGPGPG)-3') ;
Molecular weight formula_weight	6847.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TTTTTTCGGGGGGGCCCCGGGG

Entity 8 Entity 8 polymer

Description description	;DNA (5'-D(PCPCPCPCPGPGPGPGPCPCPCPCPCPCPCPGPGPC)-3') ;
Molecular weight formula_weight	5400.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

CCCCGGGGCCCCCCCGGC

Entity 9 Entity 9 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8dqzE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	8dqzE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	272 — Zinc Finger, Delta Prime; domain 3
Homologous superfamily homologous superfamily	10 —

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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	2.92 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	41190

Intermediate state of RFC:PCNA bound to a 3' ss/dsDNA junction

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

Replication factor C subunit 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

Replication factor C subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Replication factor C subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Replication factor C subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Replication factor C subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Proliferating cell nuclear antigen

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

8dqz__assembly_1__model_1

8dqz__assembly_1__model_1 | I(q)

8dqz__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 (11)

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

Entity 7 Entity 7 polymer

Polymer Polymer