SAXSdb — 8eki

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

Protein transport protein SEC20

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein transport protein USE1 × 1 （P53146） Protein transport protein TIP20 × 1 （P33891） Protein transport protein SEC39 × 1 （Q12745） Protein transport protein DSL1 × 1 （P53847）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC20_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–275； UniProt 1–275

Protein transport protein USE1

Saccharomyces cerevisiae S288C

UniProt P53146

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein transport protein SEC20 × 1 （P28791） Protein transport protein TIP20 × 1 （P33891） Protein transport protein SEC39 × 1 （Q12745） Protein transport protein DSL1 × 1 （P53847）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	USE1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–212； UniProt 1–212

Protein transport protein TIP20

Saccharomyces cerevisiae S288C

UniProt P33891

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein transport protein SEC20 × 1 （P28791） Protein transport protein USE1 × 1 （P53146） Protein transport protein SEC39 × 1 （Q12745） Protein transport protein DSL1 × 1 （P53847）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TIP20_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–701； UniProt 1–701

Protein transport protein SEC39

Saccharomyces cerevisiae S288C

UniProt Q12745

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein transport protein SEC20 × 1 （P28791） Protein transport protein USE1 × 1 （P53146） Protein transport protein TIP20 × 1 （P33891） Protein transport protein DSL1 × 1 （P53847）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC39_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–709； UniProt 1–709

Protein transport protein DSL1

Saccharomyces cerevisiae S288C

UniProt P53847

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Protein transport protein SEC20 × 1 （P28791） Protein transport protein USE1 × 1 （P53146） Protein transport protein TIP20 × 1 （P33891） Protein transport protein SEC39 × 1 （Q12745）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DSL1_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 30–783； UniProt 1–754

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	8eki
Deposition date deposition_date	2022-09-21
Structure title title	CryoEM structure of the Dsl1 complex bound to SNAREs Sec20 and Use1
Keywords keywords	Tether, SNARE, Complex, TRANSPORT PROTEIN; TRANSPORT 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.

8eki__assembly_1__model_1

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

Download this curve (.dat)

8eki__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8eki__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	80.34 Å
Rg (electron density)	81.81 Å
Total Rg	81.39 Å
Atom count	18792
Residues	2283
Excluded volume	336550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8eki__assembly_1__model_1`	pentameric （5）	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 (5)

Entity 1 Entity 1 polymer

Description description	Protein transport protein SEC20
Molecular weight formula_weight	32244.3 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	18792

MVVTFLQDLEVLQDALLNNLQKLSAISRRKESGESKHDNKDSFAAIANEHNDEEEEIEFEDLVNIIESKVSDFESVLKCSIVEMTYKYPELKLQWEKSPRYDQCDKLHIVKLDKQMNEDIYAQLVEELDFVLQFVDWFYCYRLKVKEILRQHHKRDLAWNDEKRDRAIKFHAVDYDKLHQGTSSSSSLTSTSMEKASTREKLLSKTKQLTNNLVRGNQILQSGILQSDLNLDELRAQTNSLTQIDDKYTQFETVFKKTADLVKVLENASHQEKRD

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Protein transport protein USE1
Molecular weight formula_weight	24254.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAETSNDPFLSYVLSSKQLTNLNRLRRKAVTKQLGSSDDNKVSEEFLRYQHTYQREAFEYLQTKHDAHKIMESQYEQYQSSSKTRRYSIDLDSVDAVDTESQTEYPNEEFIDRNEDSEAVMELRKRLLGKGQNKGLGYETTKSVDRQIEDQDTLQQDLIQDMSKLVGSLKQGAVAFQSALDEDKQVLGAAEIGIQVASQGLMDVSGKLRKYD

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Protein transport protein TIP20
Molecular weight formula_weight	81253.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MNGIDDLLNINDRIKQVQNERNELASKLQNLKQSLASNDTEVALSEVIAQDIIEVGASVEGLEQLRAKYGDLQILNKLEKVAVQQTQMQAGVDKLDSFERQLDELAEQPPDQFTLDDVKALHSKLTSVFATVPQINNIDSQYAAYNKLKSKVTGKYNDVIIQRLATNWSNTFDQKLLEAQWDTQKFASTSVGLVKCLRENSTKLYQLSLLYLPLEEETQNGDSERPLSRSNNNQEPVLWNFKSLANNFNVRFTYHFHATSSSSKIETYFQFLNDYLAENLYKCINIFHDDCNGLTKPVIHEQFINYVLQPIRDKVRSTLFQNDLKTLIVLISQILATDKNLLNSFHYHGLGLVSLISDEVWEKWINYEVEMANRQFINITKNPEDFPKSSQNFVKLINKIYDYLEPFYDLDFDLLVRYKLMTCSLIFMNLTSSYLDYILTVDSLNETRTKEQELYQTMAKLQHVNFVYRKIKSLSSNFIFIQLTDIVNSTESKKYNSLFQNVENDYEKAMSTDMQNSIVHRIQKLLKETLRNYFKISTWSTLEMSVDENIGPSSVPSAELVNSINVLRRLINKLDSMDIPLAISLKVKNELLNVIVNYFTESILKLNKFNQNGLNQFLHDFKSLSSILSLPSHATNYKCMSLHELVKILKLKYDPNNQQFLNPEYIKTGNFTSLKEAYSIKYLKDTKIQDALYRIIYGNIL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 polymer

Description description	Protein transport protein SEC39
Molecular weight formula_weight	82483.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MLEEQLYLLACIFASRADTRNIKKLSTRLGSQSKYLEILCVLWPELDDPKNLLFLRELEEEVQSPEGEETTDEDVIVELLESDSSLIPLIESDTTTRSNRYHELQEFISKKLNNKTLENFEEWLRERILICNEMIPETPLLYSVLWETAKSKVLSTKFIGWVEGVLKPLDHLNKRLHLIFKINEWEKMPDSELFKIIFDGVEDMQGYIGIADVIEDELAPTLSYGKKWETFITEFFNKQQFSLKSDTNYQLFIKLYYSLEKGVKDNSEASRKLQSNVVDILFHNSENLFNLSSLTHKLDELWSILSGFPDEITIEEQKTITALEMKQFMEFFIKCSTKFSFKEIFAITQEEESAQLAHFSSLCHEEFNKANEISSFLQAMYETVLDISKDDKIFTRISMDEKLYSILEILLQMNEFAYIEAIIERFDYSNNTQIYELLVKFFWHFFNNASNGLRKEPEMKKASQTLQIIQKHMSQRAGTNLTKLEVLLEISDKLSHYSINLNKSHNGARDTAFKPSNILEYRDCPLDIISNLLELNPRLYKDLPTTKSLLFGIYDSLSINREGQTGKVEVDLMVLHIDYALVNLDFGTAYELGKQVFEICQEAGQHMMKALGDEHWLTFYQMGKFVDPNWVDNEIPTEIIVLQMSILGRLLEVCPLEEVEIVTSQWSTLELELSARDLVKDKYALDGQNDNKSKVGGIAREIFHNVTNF

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21

Entity 5 Entity 5 polymer

Description description	Protein transport protein DSL1
Molecular weight formula_weight	91445.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MKHHHHHHHGAAGTSLYKKAGENLYFQGSMESLFPNKGEIIRELLKDPLILKNDSKRSNGSELELDSSDLLQREAILANELNILDNLKTFLNLIKEVKTNLNILELENCYYSLQSLRKKMRNNAAYLKQSFNFQQSISTYVDTLHLELVSTLYKILTNGFWKITENSIQFTPTVEWGKDKVHIEYDTFMDFVAQQYFPKGSLDNQAWFILDMTSADSQEQVRAKLNTIMKEYMNLSRIVSMIKNSIFISGKEISYENEKNILVFSKSSSHGQHCVSTVLTSFEAVCDFMLDGLAFRDRKTLSYELGPLFNTEFTKFVKNNASIILESLDSPLKNLVSVINNKLTRLVAKSEVTNWTHSGKEIQDLLMNKQLYYNLLLDKVLESHISEIRSIFEDPKKSWQNLEVVELTTSNTNTMSEKIGKNDSDVQNEKELHNAVSKDDDWNWEVEDDDADAWGDEIDVNIDDEEEKTNQEKEKEPEEEENAWDEAWAIDENIDDASLENGKEHLKAHDVGSLDKDHIEVTQLPKLFLAISQNFKSSFADSHVDEQYFAYKYNLLQTSYMAMCTANFSHNWCQLYVDMRYLIERDEKLYRIKELTRNLLETKLNMKYRIVCQLIRHQLTEFRENERNPSWDATIEKLLPYILKEIVRPLQKIRGEEGSRYLLSFLNFLYNDCVTKEILKWQIISEVNSENLGELVSLLVNNTDIQLLAKEPSYKKMREKFATMGKFLPLHLKEIMEMFYNGDFYLFATDELIQWIELLFADTPLRRNAIDDIYEIRGTALDD

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21

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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	4.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	49947

CryoEM structure of the Dsl1 complex bound to SNAREs Sec20 and Use1

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

Protein transport protein SEC20

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein USE1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein TIP20

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein SEC39

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein transport protein DSL1

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

8eki__assembly_1__model_1

8eki__assembly_1__model_1 | I(q)

8eki__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 (5)

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

7. Citations (1)