8twb

Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-DNA complex

Method: ELECTRON MICROSCOPY

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

Replication factor C subunit 4

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 3 × 1 （P38629） Replication factor C subunit 2 × 1 （P40348） Replication factor C subunit 5 × 1 （P38251） Chromosome transmission fidelity protein 18 × 1 （P49956） Proliferating cell nuclear antigen × 3 （P15873） Template DNA × 1 Primer DNA × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3 ADENOSINE-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	1
Chains and sequence ranges	Author chain 4； PDBConstruct 1–319； UniProt 4–322

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 4 × 1 （P40339） Replication factor C subunit 2 × 1 （P40348） Replication factor C subunit 5 × 1 （P38251） Chromosome transmission fidelity protein 18 × 1 （P49956） Proliferating cell nuclear antigen × 3 （P15873） Template DNA × 1 Primer DNA × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3 ADENOSINE-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	2
Chains and sequence ranges	Author chain 3； PDBConstruct 1–327； UniProt 9–335

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 4 × 1 （P40339） Replication factor C subunit 3 × 1 （P38629） Replication factor C subunit 5 × 1 （P38251） Chromosome transmission fidelity protein 18 × 1 （P49956） Proliferating cell nuclear antigen × 3 （P15873） Template DNA × 1 Primer DNA × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3 ADENOSINE-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	3
Chains and sequence ranges	Author chain 2； PDBConstruct 1–340； UniProt 14–353

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 4 × 1 （P40339） Replication factor C subunit 3 × 1 （P38629） Replication factor C subunit 2 × 1 （P40348） Chromosome transmission fidelity protein 18 × 1 （P49956） Proliferating cell nuclear antigen × 3 （P15873） Template DNA × 1 Primer DNA × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3 ADENOSINE-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	4
Chains and sequence ranges	Author chain 5； PDBConstruct 4–353； UniProt 4–353

Chromosome transmission fidelity protein 18

Saccharomyces cerevisiae

UniProt P49956

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） Template DNA × 1 Primer DNA × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CTF18_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 1； PDBConstruct 1–258； UniProt 386–643

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 4 × 1 （P40339） Replication factor C subunit 3 × 1 （P38629） Replication factor C subunit 2 × 1 （P40348） Replication factor C subunit 5 × 1 （P38251） Chromosome transmission fidelity protein 18 × 1 （P49956） Template DNA × 1 Primer DNA × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3 ADENOSINE-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 A； PDBConstruct 1–258； UniProt 1–258 Author chain B； PDBConstruct 1–258； UniProt 1–258 Author chain C； PDBConstruct 1–258； 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	8twb
Deposition date deposition_date	2023-08-20
Structure title title	Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-DNA complex
Keywords keywords	Ctf18, RFC2-5, PCNA, DNA, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/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.

8twb__assembly_1__model_1

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

Download this curve (.dat)

8twb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8twb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.29 Å
Rg (electron density)	41.98 Å
Total Rg	42.32 Å
Atom count	19167
Residues	2387
Excluded volume	340090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8twb__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 4
Molecular weight formula_weight	35782.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4
Atom count atom_count	19167

TLSLQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQSNKIIEPLQSRCAILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEGDMRQAINNLQSTVAGHGLVNADNVFKIVDSPHPLIVKKMLLASNLEDSIQILRTDLWKKGYSSIDIVTTSFRVTKNLAQVKESVRLEMIKEIGLTHMRILEGVGTYLQLASMLAKIHKLNNK

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer'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 3
Molecular weight formula_weight	36818.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

SKENLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAHKLTPALLSRCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNGDMRRVLNVLQSCKATLDNPDEDEISDDVIYECCGAPRPSDLKAVLKSILEDDWGTAHYTLNKVRSAKGLALIDLIEGIVKILEDYELQNEETRVHLLTKLADIEYSISKGGNDQIQGSAVIGAIKASFENET

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer'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 2
Molecular weight formula_weight	38256.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

SKLAAEQSLAQQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSALRRTMETYSGVTRFCLICNYVTRIIDPLASRCSKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAGDLRRGITLLQSASKGAQYLGDGKNITSTQVEELAGVVPHDILIEIVEKVKSGDFDEIKKYVNTFMKSGWSAASVVNQLHEYYITNDNFDTNFKNQISWLLFTTDSRLNNGTNEHIQLLNLLVKISQL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer'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 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	5

MSLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQAALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTILSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSSSPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIILKELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMCCLD

Source Source

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

Entity 5 Entity 5 polymer

Description description	Chromosome transmission fidelity protein 18
Molecular weight formula_weight	30182.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1

NTWASSNKDSPISWFKIVNQLFRKDPHRDIKEQFYELLNQVELNGNSDRILQGCFNIFPYVKYSDNGIRKPANISDWLFFHDLMYQSMYAHNGELLRYSALVPLVFFQTFGDIANKDDIRMKNSEYEQRELKRANSDIVSLIMRHISVQSPLMASFTDRKSLIFEILPYLDSMISSDFNKIRNLKLKQAIMEELVQLLKSFQLNLIQNRSEGFDVRGGLTIDPPIDEVVLLNPKHINEVQHKRANNLSSLLAKIEENR

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer'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	28944.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

MLEAKFEEASLFKRIIDGFKDCVQLVNFQCKEDGIIAQAVDDSRVLLVSLEIGVEAFQEYRCDHPVTLGMDLTSLSKILRCGNNTDTLTLIADNTPDSIILLFEDTKKDRIAEYSLKLMDIDADFLKIEELQYDSTLSLPSSEFSKIVRDLSQLSDSINIMITKETIKFVADGDIGSGSVIIKPFVDMEHPETSIKLEMDQPVDLTFGAKYLLDIIKGSSLSDRVGIRLSSEAPALFQFDLKSGFLQFFLAPKFNDEE

Source Source

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

Entity 7 Entity 7 polymer

Description description	Template DNA
Molecular weight formula_weight	5542.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

AGCAGCAACAGAGAATCT

Entity 8 Entity 8 polymer

Description description	Primer DNA
Molecular weight formula_weight	5184.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

AGATTCTCTGTTGCTGC

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	3

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	3

Entity 11 Entity 11 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

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Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	115411

Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-DNA complex

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

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

Chromosome transmission fidelity protein 18

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

8twb__assembly_1__model_1

8twb__assembly_1__model_1 | I(q)

8twb__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 (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

Entity 8 Entity 8 polymer

Polymer Polymer