7q5b

Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene

Method: ELECTRON MICROSCOPY

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

Transposon Ty3-G Gag-Pol polyprotein

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 6	DNA (56-MER) × 1 DNA (31-MER) × 1 DNA (34-MER) × 1 DNA (9-MER) × 1 ;Transcription factor TFIIIB component B'' ; × 1 （P46678） TATA-box-binding protein × 1 （P13393） Transcription factor IIIB 70 kDa subunit × 1 （P29056） DNA (19-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YG31B_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain A； PDBConstruct 1–1547； UniProt 1–1547 Author chain B； PDBConstruct 1–1547； UniProt 1–1547 Author chain C； PDBConstruct 1–1547； UniProt 1–1547 Author chain D； PDBConstruct 1–1547； UniProt 1–1547

;Transcription factor TFIIIB component B'' ;

Saccharomyces cerevisiae S288C

UniProt P46678

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 6	DNA (56-MER) × 1 DNA (31-MER) × 1 DNA (34-MER) × 1 DNA (9-MER) × 1 Transposon Ty3-G Gag-Pol polyprotein × 4 （Q99315） TATA-box-binding protein × 1 （P13393） Transcription factor IIIB 70 kDa subunit × 1 （P29056） DNA (19-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TFC5_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain X； PDBConstruct 1–594； UniProt 1–594

TATA-box-binding protein

Saccharomyces cerevisiae S288C

UniProt P13393

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 6	DNA (56-MER) × 1 DNA (31-MER) × 1 DNA (34-MER) × 1 DNA (9-MER) × 1 Transposon Ty3-G Gag-Pol polyprotein × 4 （Q99315） ;Transcription factor TFIIIB component B'' ; × 1 （P46678） Transcription factor IIIB 70 kDa subunit × 1 （P29056） DNA (19-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBP_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain Y； PDBConstruct 1–240； UniProt 1–240

Transcription factor IIIB 70 kDa subunit

Saccharomyces cerevisiae S288C

UniProt P29056

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 7 DNA 6	DNA (56-MER) × 1 DNA (31-MER) × 1 DNA (34-MER) × 1 DNA (9-MER) × 1 Transposon Ty3-G Gag-Pol polyprotein × 4 （Q99315） ;Transcription factor TFIIIB component B'' ; × 1 （P46678） TATA-box-binding protein × 1 （P13393） DNA (19-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF3B_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain Z； PDBConstruct 1–596； UniProt 1–596

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	7q5b
Deposition date deposition_date	2021-11-03
Structure title title	Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene
Keywords keywords	Transcription, RNA Pol III, Ty3 Retrotransposon, Intasome, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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.

7q5b__assembly_1__model_1

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

Download this curve (.dat)

7q5b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7q5b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.94 Å
Rg (electron density)	52.40 Å
Total Rg	52.53 Å
Atom count	21746
Residues	2423
Excluded volume	377820 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7q5b__assembly_1__model_1`	tridecameric （13）	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 (9)

Entity 1 Entity 1 polymer

Description description	DNA (56-MER)
Molecular weight formula_weight	17165.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	R
Atom count atom_count	21746

GAGCCCGTAATACAACAGATTTTTTCTCTTAGTTTTAAATTTTTATATTTCGTCGA

Entity 2 Entity 2 polymer

Description description	DNA (31-MER)
Molecular weight formula_weight	9484.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	S

GAGCCCGTAATACAACAAAATCCAACAAATA

Entity 3 Entity 3 polymer

Description description	DNA (34-MER)
Molecular weight formula_weight	10532.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	r

TCGACGAAATATAAAAATTTAAAACTAAGAGAAA

Entity 4 Entity 4 polymer

Description description	DNA (9-MER)
Molecular weight formula_weight	2751.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	s

TATTTGTTG

Entity 5 Entity 5 polymer

Description description	Transposon Ty3-G Gag-Pol polyprotein
Molecular weight formula_weight	178556.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MSFMDQIPGGGNYPKLPVECLPNFPIQPSLTFRGRNDSHKLKNFISEIMLNMSMISWPNDASRIVYCRRHLLNPAAQWANDFVQEQGILEITFDTFIQGLYQHFYKPPDINKIFNAITQLSEAKLGIERLNQRFRKIWDRMPPDFMTEKAAIMTYTRLLTKETYNIVRMHKPETLKDAMEEAYQTTALTERFFPGFELDADGDTIIGATTHLQEEYDSDYDSEDNLTQNGYVHTVRTRRSYNKPMSNHRNRRNNNPSREECIKNRLCFYCKKEGHRLNECRARKAVLTDLELESKDQQTPFIKTLPIVHYIAIPEMDNTAEKTIKIQNTKVKTLFDSGSPTSFIRRDIVELLKYEIYETPPLRFRGFVATKSAVTSEAVTIDLKINDLHITLAAYILDNMDYQLLIGNPILRRYPKILHTVLNTRESPDSLKPKTYRSETVNNVRTYSAGNRGNPRNIKLSFAPTILEATDPKSAGNRGDSRTKTLSLATTTPAAIDPLTTLDNPGSTQSTFAQFPIPEEASILEEDGKYSNVVSTIQSVEPNATDHSNKDTFCTLPVWLQQKYREIIRNDLPPRPADINNIPVKHDIEIKPGARLPRLQPYHVTEKNEQEINKIVQKLLDNKFIVPSKSPCSSPVVLVPKKDGTFRLCVDYRTLNKATISDPFPLPRIDNLLSRIGNAQIFTTLDLHSGYHQIPMEPKDRYKTAFVTPSGKYEYTVMPFGLVNAPSTFARYMADTFRDLRFVNVYLDDILIFSESPEEHWKHLDTVLERLKNENLIVKKKKCKFASEETEFLGYSIGIQKIAPLQHKCAAIRDFPTPKTVKQAQRFLGMINYYRRFIPNCSKIAQPIQLFICDKSQWTEKQDKAIDKLKDALCNSPVLVPFNNKANYRLTTDASKDGIGAVLEEVDNKNKLVGVVGYFSKSLESAQKNYPAGELELLGIIKALHHFRYMLHGKHFTLRTDHISLLSLQNKNEPARRVQRWLDDLATYDFTLEYLAGPKNVVADAISRAVYTITPETSRPIDTESWKSYYKSDPLCSAVLIHMKELTQHNVTPEDMSAFRSYQKKLELSETFRKNYSLEDEMIYYQDRLVVPIKQQNAVMRLYHDHTLFGGHFGVTVTLAKISPIYYWPKLQHSIIQYIRTCVQCQLIKSHRPRLHGLLQPLPIAEGRWLDISMDFVTGLPPTSNNLNMILVVVDRFSKRAHFIATRKTLDATQLIDLLFRYIFSYHGFPRTITSDRDVRMTADKYQELTKRLGIKSTMSSANHPQTDGQSERTIQTLNRLLRAYASTNIQNWHVYLPQIEFVYNSTPTRTLGKSPFEIDLGYLPNTPAIKSDDEVNARSFTAVELAKHLKALTIQTKEQLEHAQIEMETNNNQRRKPLLLNIGDHVLVHRDAYFKKGAYMKVQQIYVGPFRVVKKINDNAYELDLNSHKKKHRVINVQFLKKFVYRPDAYPKNKPISSTERIKRAHEVTALIGIDTTHKTYLCHMQDVDPTLSVEYSEAEFCQIPERTRRSILANFRQLYETQDNPEREEDVVSQNEICQYDNTSP

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	;Transcription factor TFIIIB component B'' ;
Molecular weight formula_weight	67801.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MSSIVNKSGTRFAPKVRQRRAATGGTPTPKPRTPQLFIPESKEIEEDNSDNDKGVDENETAIVEKPSLVGERSLEGFTLTGTNGHDNEIGDEGPIDASTQNPKADVIEDNVTLKPAPLQTHRDQKVPRSSRLASLSKDNESRPSFKPSFLDSSSNSNGTARRLSTISNKLPKKIRLGSITENDMNLKTFKRHRVLGKPSSAKKPAGAHRISIVSKISPPTAMTDSLDRNEFSSETSTSREADENENYVISKVKDIPKKVRDGESAKYFIDEENFTMAELCKPNFPIGQISENFEKSKMAKKAKLEKRRHLRELRMRARQEFKPLHSLTKEEQEEEEEKRKEERDKLLNADIPESDRKAHTAIQLKLNPDGTMAIDEETMVVDRHKNASIENEYKEKVDENPFANLYNYGSYGRGSYTDPWTVEEMIKFYKALSMWGTDFNLISQLYPYRSRKQVKAKFVNEEKKRPILIELALRSKLPPNFDEYCCEIKKNIGTVADFNEKLIELQNEHKHHMKEIEEAKNTAKEEDQTAQRLNDANLNKKGSGGIMTNDLKVYRKTEVVLGTIDDLKRKKLKERNNDDNEDNEGSEEEPEIDQ

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	TATA-box-binding protein
Molecular weight formula_weight	27042.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MADEERLKEFKEANKIVFDPNTRQVWENQNRDGTKPATTFQSEEDIKRAAPESEKDTSATSGIVPTLQNIVATVTLGCRLDLKTVALHARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAAKFTDFKIQNIVGSCDVKFPIRLEGLAFSHGTFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQREEIYQAFEAIYPVLSEFRKM

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Transcription factor IIIB 70 kDa subunit
Molecular weight formula_weight	67011.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

MPVCKNCHGTEFERDLSNANNDLVCKACGVVSEDNPIVSEVTFGETSAGAAVVQGSFIGAGQSHAAFGGSSALESREATLNNARRKLRAVSYALHIPEYITDAAFQWYKLALANNFVQGRRSQNVIASCLYVACRKEKTHHMLIDFSSRLQVSVYSIGATFLKMVKKLHITELPLADPSLFIQHFAEKLDLADKKIKVVKDAVKLAQRMSKDWMFEGRRPAGIAGACILLACRMNNLRRTHTEIVAVSHVAEETLQQRLNEFKNTKAAKLSVQKFRENDVEDGEARPPSFVKNRKKERKIKDSLDKEEMFQTSEEALNKNPILTQVLGEQELSSKEVLFYLKQFSERRARVVERIKATNGIDGENIYHEGSENETRKRKLSEVSIQNEHVEGEDKETEGTEEKVKKVKTKTSEEKKENESGHFQDAIDGYSLETDPYCPRNLHLLPTTDTYLSKVSDDPDNLEDVDDEELNAHLLNEEASKLKERIWIGLNADFLLEQESKRLKQEADIATGNTSVKKKRTRRRNNTRSDEPTKTVDAAAAIGLMSDLQDKSGLHAALKAAEESGDFTTADSVKNMLQKASFSKKINYDAIDGLFR

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	DNA (19-MER)
Molecular weight formula_weight	5882.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	t,u

GGTGTTGTATTACGGGCTC

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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	triclinic

Resolution resolution	3.98 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	101469

Cryo-EM structure of Ty3 retrotransposon targeting a TFIIIB-bound tRNA gene

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

Transposon Ty3-G Gag-Pol polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Transcription factor TFIIIB component 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

TATA-box-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcription factor IIIB 70 kDa subunit

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

7q5b__assembly_1__model_1

7q5b__assembly_1__model_1 | I(q)

7q5b__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

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

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 polymer

Polymer Polymer

7. Citations (1)