7zgr

Polymerase module of yeast CPF in complex with Mpe1, the yPIM of Cft2 and the pre-cleaved CYC1 RNA

Method: ELECTRON MICROSCOPY

▼

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

Protein CFT1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	;mRNA 3'-end-processing protein YTH1 ; × 1 （A0A6A5Q2R8） Cleavage factor two protein 2 × 1 （Q12102） Polyadenylation factor subunit 2 × 1 （A0A6A5Q543） pre-cleaved CYC1 × 1 MPE1 isoform 1 × 1 （A0A6A5PV64） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CFT1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1357； UniProt 1–1357

;mRNA 3'-end-processing protein YTH1 ;

Saccharomyces cerevisiae

UniProt A0A6A5Q2R8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	Protein CFT1 × 1 （Q06632） Cleavage factor two protein 2 × 1 （Q12102） Polyadenylation factor subunit 2 × 1 （A0A6A5Q543） pre-cleaved CYC1 × 1 MPE1 isoform 1 × 1 （A0A6A5PV64） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q2R8_YEASX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–208； UniProt 1–208

Cleavage factor two protein 2

Saccharomyces cerevisiae

UniProt Q12102

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	Protein CFT1 × 1 （Q06632） ;mRNA 3'-end-processing protein YTH1 ; × 1 （A0A6A5Q2R8） Polyadenylation factor subunit 2 × 1 （A0A6A5Q543） pre-cleaved CYC1 × 1 MPE1 isoform 1 × 1 （A0A6A5PV64） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CFT2_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–720； UniProt 1–720

Polyadenylation factor subunit 2

Saccharomyces cerevisiae

UniProt A0A6A5Q543

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	Protein CFT1 × 1 （Q06632） ;mRNA 3'-end-processing protein YTH1 ; × 1 （A0A6A5Q2R8） Cleavage factor two protein 2 × 1 （Q12102） pre-cleaved CYC1 × 1 MPE1 isoform 1 × 1 （A0A6A5PV64） ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q543_YEASX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–465； UniProt 1–465

MPE1 isoform 1

Saccharomyces cerevisiae

UniProt A0A6A5PV64

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 5 RNA 1	Protein CFT1 × 1 （Q06632） ;mRNA 3'-end-processing protein YTH1 ; × 1 （A0A6A5Q2R8） Cleavage factor two protein 2 × 1 （Q12102） Polyadenylation factor subunit 2 × 1 （A0A6A5Q543） pre-cleaved CYC1 × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5PV64_YEASX
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–441； UniProt 1–441

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7zgr
Deposition date deposition_date	2022-04-04
Structure title title	Polymerase module of yeast CPF in complex with Mpe1, the yPIM of Cft2 and the pre-cleaved CYC1 RNA
Keywords keywords	;CPF, 3'-end processing, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

7zgr__assembly_1__model_1

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

Download this curve (.dat)

7zgr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zgr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.35 Å
Rg (electron density)	37.88 Å
Total Rg	38.29 Å
Atom count	14505
Residues	1823
Excluded volume	259040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zgr__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Protein CFT1
Molecular weight formula_weight	153577.2 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	14505

MNVYDDVLDATVVSHSLATHFTTSDYEELLVVRTNILSVYRPTRDGKLYLTDEFKFHGLITDIGLIPQKDSPLSCLLLCTGVAKISILKFNTLTNSIDTLSLHYYEGKFKGKSLVELAKISTLRMDPGSSCALLFNNDIIAFLPFHVNKNDDDEEEEDEDENIDDSELIHSMNQKSQGTNTFNKRKRTKLGDKFTAPSVVLVASELYEGAKNIIDIQFLKNFTKPTIALLYQPKLVWAGNTTISKLPTQYVILTLNIQPAESATKIESTTIAFVKELPWDLHTIVPVSNGAIIVGTNELAFLDNTGVLQSTVLLNSFADKELQKTKIINNSSLEIMFREKNTTSIWIPSSKSKNGGSNNDETLLLMDLKSNIYYIQMEAEGRLLIKFDIFKLPIVNDLLKENSNPKCITRLNATNSNKNMDLFIGFGSGNALVLRLNNLKSTIETREAHNPSSGTNSLMDINDDDDEEMDDLYADEAPENGLTTNDSKGTVETVQPFDIELLSSLRNVGPITSLTVGKVSSIDDVVKGLPNPNKNEYSLVATSGNGSGSHLTVIQTSVQPEIELALKFISITQIWNLKIKGRDRYLITTDSTKSRSDIYESDNNFKLHKGGRLRRDATTVYISMFGEEKRIIQVTTNHLYLYDTHFRRLTTIKFDYEVIHVSVMDPYILVTVSRGDIKIFELEEKNKRKLLKVDLPEILNEMVITSGLILKSNMCNEFLIGLSKSQEEQLLFTFVTADNQIIFFTKDHNDRIFQLNGVDQLNESLYISTYQLGDEIVPDPSIKQVMINKLGHDNKEEYLTILTFGGEIYQYRKLPQRRSRFYRNVTRNDLAITGAPDNAYAKGVSSIERIMHYFPDYNGYSVIFVTGSVPYILIKEDDSTPKIFKFGNIPLVSVTPWSERSVMCVDDIKNARVYTLTTDNMYYGNKLPLKQIKISNVLDDYKTLQKLVYHERAQLFLVSYCKRVPYEALGEDGEKVIGYDENVPHAEGFQSGILLINPKSWKVIDKIDFPKNSVVNEMRSSMIQINSKTKRKREYIIAGVANATTEDTPPTGAFHIYDVIEVVPEPGKPDTNYKLKEIFQEEVSGTVSTVCEVSGRFMISQSQKVLVRDIQEDNSVIPVAFLDIPVFVTDSKSFGNLLIIGDAMQGFQFIGFDAEPYRMISLGRSMSKFQTMSLEFLVNGGDMYFAATDADRNVHVLKYAPDEPNSLSGQRLVHCSSFTLHSTNSCMMLLPRNEEFGSPQVPSFQNVGGQVDGSVFKIVPLSEEKYRRLYVIQQQIIDRELQLGGLNPRMERLANDFYQMGHSMRPMLDFNVIRRFCGLAIDRRKSIAQKAGRHAHFEAWRDIINIEFSMRSLCQGK

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	;mRNA 3'-end-processing protein YTH1 ;
Molecular weight formula_weight	24594.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSLIHPDTAKYPFKFEPFLRQEYSFSLDPDRPICEFYNSREGPKSCPRGPLCPKKHVLPIFQNKIVCRHWLRGLCKKNDQCEYLHEYNLRKMPECVFFSKNGYCTQSPDCQYLHIDPASKIPKCENYEMGFCPLGSSCPRRHIKKVFCQRYMTGFCPLGKDECDMEHPQFIIPDEGSKLRIKRDDEINTRKMDEEKERRLNAIINGEV

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	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Cleavage factor two protein 2
Molecular weight formula_weight	80993.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MTYKYNCCDDGSGTTVGSVVRFDNVTLLIDPGWNPSKVSYEQCIKYWEKVIPEIDVIILSQPTIECLGAHSLLYYNFTSHFISRIQVYATLPVINLGRVSTIDSYASAGVIGPYDTNKLDLEDIEISFDHIVPLKYSQLVDLRSRYDGLTLLAYNAGVCPGGSIWCISTYSEKLVYAKRWNHTRDNILNAASILDATGKPLSTLMRPSAIITTLDRFGSSQPFKKRSKIFKDTLKKGLSSDGSVIIPVDMSGKFLDLFTQVHELLFESTKINAHTQVPVLILSYARGRTLTYAKSMLEWLSPSLLKTWENRNNTSPFEIGSRIKIIAPNELSKYPGSKICFVSEVGALINEVIIKVGNSEKTTLILTKPSFECASSLDKILEIVEQDERNWKTFPEDGKSFLCDNYISIDTIKEEPLSKEETEAFKVQLKEKKRDRNKKILLVKRESKKLANGNAIIDDTNGERAMRNQDILVENVNGVPPIDHIMGGDEDDDEEEENDNLLNLLKDNSEKSAAKKNTEVPVDIIIQPSAASKHKMFPFNPAKIKKDDYGTVVDFTMFLPDDSDNVNQNSRKRPLKDGAKTTSPVNEEDNKNEEEDGYNMSDPISKRSKHRASRYSGFSGTGEAENFDNLDYLKIDKTLSKRTISTVNVQLKCSVVILNLQSLVDQRSASIIWPSLKSRKIVLSAPKQIQNEEITAKLIKKNIEVVNMPLNKIVEFSTTI

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	Spodoptera frugiperda

Entity 4 Entity 4 polymer

Description description	Polyadenylation factor subunit 2
Molecular weight formula_weight	53211.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MDGHNQNQYQNQNQIQQSQQPPLKKYVTQRRSVDVSSPYINLYYNRRHGLPNLVVEPETSYTIDIMPPNAYRGRDRVINLPSKFTHLSSNKVKHVIPAIQWTPEGRRLVVATYSGEFSLWNASSFTFETLMQAHDSAVTTMKYSHDSDWMISGDADGMIKIWQPNFSMVKEIDAAHTESIRDMAFSSNDSKFVTCSDDNILKIWNFSNGKQERVLSGHHWDVKSCDWHPEMGLIASASKDNLVKLWDPRSGNCISSILKFKHTVLKTRFQPTKGNLLMAISKDKSCRVFDIRYSMKELMCVRDETDYMTLEWHPINESMFTLACYDGSLKHFDLLQNLNEPILTIPYAHDKCITSLSYNPVGHIFATAAKDRTIRFWTRARPIDPNAYDDPTYNNKKINGWFFGINNDINAVREKSEFGAAPPPPATLEPHALPNMNGFINKKPRQEIPGIDSNIKSSTLPGLSI

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	Spodoptera frugiperda

Entity 5 Entity 5 polymer

Description description	pre-cleaved CYC1
Molecular weight formula_weight	13329.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

UUUAUAGUUAUGUUAGUAUUAAGAACGUUAUUUAUAUUUCAA

Entity 6 Entity 6 polymer

Description description	MPE1 isoform 1
Molecular weight formula_weight	49711.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSSTIFYRFKSQRNTSRILFDGTGLTVFDLKREIIQENKLGDGTDFQLKIYNPDTEEEYDDDAFVIPRSTSVIVKRSPAIKSFSVHSRLKGNVGAAALGNATRYVTGRPRVLQKRQHTATTTANVSGTTEEERIASMFATQENQWEQTQEEMSAATPVFFKSQTNKNSAQENEGPPPPGYMCYRCGGRDHWIKNCPTNSDPNFEGKRIRRTTGIPKKFLKSIEIDPETMTPEEMAQRKIMITDEGKFVVQVEDKQSWEDYQRKRENRQIDGDETIWRKGHFKDLPDDLKCPLTGGLLRQPVKTSKCCNIDFSKEALENALVESDFVCPNCETRDILLDSLVPDQDKEKEVETFLKKQEELHGSSKDGNQPETKKMKLMDPTGTAGLNNNTSLPTSVNNGGTPVPPVPLPFGIPPFPMFPMPFMPPTATITNPHQADASPKK

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	Spodoptera frugiperda

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	2

▶

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	2.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	846349

Polymerase module of yeast CPF in complex with Mpe1, the yPIM of Cft2 and the pre-cleaved CYC1 RNA

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

Protein CFT1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;mRNA 3'-end-processing protein YTH1 ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cleavage factor two protein 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

Polyadenylation factor 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

MPE1 isoform 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

7zgr__assembly_1__model_1

7zgr__assembly_1__model_1 | I(q)

7zgr__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

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

7. Citations (1)