8yjz

Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D

Method: ELECTRON MICROSCOPY

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

Proliferating cell nuclear antigen

Homo sapiens

UniProt P12004

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 3	Flap endonuclease 1 × 1 （P39748） Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） upstream DNA × 1 parent strand DNA × 1 downstream DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PCNA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–261； UniProt 1–261 Author chain B； PDBConstruct 1–261； UniProt 1–261 Author chain C； PDBConstruct 1–261； UniProt 1–261

Flap endonuclease 1

OrganismNot specified

UniProt P39748

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 3	Proliferating cell nuclear antigen × 3 （P12004） Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） upstream DNA × 1 parent strand DNA × 1 downstream DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FEN1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–380； UniProt 1–380

Ribonuclease H2 subunit A

OrganismNot specified

UniProt O75792

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 3	Proliferating cell nuclear antigen × 3 （P12004） Flap endonuclease 1 × 1 （P39748） Ribonuclease H2 subunit B × 1 （Q5TBB1） Ribonuclease H2 subunit C × 1 （Q8TDP1） upstream DNA × 1 parent strand DNA × 1 downstream DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNH2A_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–299； UniProt 1–299

Ribonuclease H2 subunit B

OrganismNot specified

UniProt Q5TBB1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 3	Proliferating cell nuclear antigen × 3 （P12004） Flap endonuclease 1 × 1 （P39748） Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit C × 1 （Q8TDP1） upstream DNA × 1 parent strand DNA × 1 downstream DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNH2B_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 1–312； UniProt 1–312

Ribonuclease H2 subunit C

OrganismNot specified

UniProt Q8TDP1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 3	Proliferating cell nuclear antigen × 3 （P12004） Flap endonuclease 1 × 1 （P39748） Ribonuclease H2 subunit A × 1 （O75792） Ribonuclease H2 subunit B × 1 （Q5TBB1） upstream DNA × 1 parent strand DNA × 1 downstream DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNH2C_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–164； UniProt 1–164

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	8yjz
Deposition date deposition_date	2024-03-03
Structure title title	Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D
Keywords keywords	Flap endonuclease 1, RNase H2, endogenous DNA, PCNA, DNA BINDING PROTEIN/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.

8yjz__assembly_1__model_1

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

Download this curve (.dat)

8yjz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yjz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.64 Å
Rg (electron density)	42.78 Å
Total Rg	42.99 Å
Atom count	14948
Residues	1809
Excluded volume	263310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yjz__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 (8)

Entity 1 Entity 1 polymer

Description description	Proliferating cell nuclear antigen
Molecular weight formula_weight	28795.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,A
Atom count atom_count	14948

MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGS

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Flap endonuclease 1
Molecular weight formula_weight	42661.1 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFFKVTGSLSSAKRKEPEPKGSTKKKAKTGAAGKFKRGK

Entity 3 Entity 3 polymer

Description description	Ribonuclease H2 subunit A
Molecular weight formula_weight	33431.8 kDa
EC 编号 ec_number	3.1.26.4
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MDLSELERDNTGRCRLSSPVPAVCRKEPCVLGVDEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDTDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMPETYQARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDYGSGYPNDPKTKAWLKEHVEPVFGFPQFVRFSWRTAQTILEKEAEDVIWEDSASENQEGLRKITSYFLNEGSQARPRSSHRYFLERGLESATSL

Entity 4 Entity 4 polymer

Description description	Ribonuclease H2 subunit B
Molecular weight formula_weight	35195.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MAAGVDCGDGVGARQHVFLVSEYLKDASKKMKNGLMFVKLVNPCSGEGAIYLFNMCLQQLFEVKVFKEKHHSWFINQSVQSGGLLHFATPVDPLFLLLHYLIKADKEGKFQPLDQVVVDNVFPNCILLLKLPGLEKLLHHVTEEKGNPEIDNKKYYKYSKEKTLKWLEKKVNQTVAALKTNNVNVSSRVQSTAFFSGDQASTDKEEDYIRYAHGLISDYIPKELSDDLSKYLKLPEPSASLPNPPSKKIKLSDEPVEAKEDYTKFNTKDLKTEKKNSKMTAAQKALAKVDKSGMKSIDTFFGVKNKKKIGKV

Entity 5 Entity 5 polymer

Description description	Ribonuclease H2 subunit C
Molecular weight formula_weight	17862.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MESGDEAAIERHRVHLRSATLRDAVPATLHLLPCEVAVDGPAPVGRFFTPAIRQGPEGLEVSFRGRCLRGEEVAVPPGLVGYVMVTEEKKVSMGKPDPLRDSGTDDQEEEPLERDFDRFIGATANFSRFTLWGLETIPGPDAKVRGALTWPSLAAAIHAQVPED

Entity 6 Entity 6 polymer

Description description	upstream DNA
Molecular weight formula_weight	6102.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATTTTTAATTTATAATTATT

Entity 7 Entity 7 polymer

Description description	parent strand DNA
Molecular weight formula_weight	9565.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

ATTTTAAAAAAAATAATTATAAATTAAAAAT

Entity 8 Entity 8 polymer

Description description	downstream DNA
Molecular weight formula_weight	4249.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

TTTTTTTTTAAAAT

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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	5.15 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	13906

Structure of the human endogenous PCNA-FEN1-RNase H2 complex - State D

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

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

Flap endonuclease 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

Ribonuclease H2 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

Ribonuclease H2 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

Ribonuclease H2 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8yjz__assembly_1__model_1

8yjz__assembly_1__model_1 | I(q)

8yjz__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

7. Citations (1)