SAXSdb — 5dfz

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

Vacuolar protein sorting-associated protein 38

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Phosphatidylinositol 3-kinase VPS34 × 1 （P22543） Serine/threonine-protein kinase VPS15 × 1 （P22219） Nanobody binding S. cerevisiae Vps34 × 1 Vacuolar protein sorting-associated protein 30 × 1 （Q02948） Putative N-terminal domain of S. cerevisiae Vps30 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS38_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–439； UniProt 1–439

Phosphatidylinositol 3-kinase VPS34

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P22543

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Vacuolar protein sorting-associated protein 38 × 1 （Q05919） Serine/threonine-protein kinase VPS15 × 1 （P22219） Nanobody binding S. cerevisiae Vps34 × 1 Vacuolar protein sorting-associated protein 30 × 1 （Q02948） Putative N-terminal domain of S. cerevisiae Vps30 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS34_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–875； UniProt 1–875

Serine/threonine-protein kinase VPS15

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P22219

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Vacuolar protein sorting-associated protein 38 × 1 （Q05919） Phosphatidylinositol 3-kinase VPS34 × 1 （P22543） Nanobody binding S. cerevisiae Vps34 × 1 Vacuolar protein sorting-associated protein 30 × 1 （Q02948） Putative N-terminal domain of S. cerevisiae Vps30 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VPS15_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–1444； UniProt 1–1454

Vacuolar protein sorting-associated protein 30

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q02948

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Vacuolar protein sorting-associated protein 38 × 1 （Q05919） Phosphatidylinositol 3-kinase VPS34 × 1 （P22543） Serine/threonine-protein kinase VPS15 × 1 （P22219） Nanobody binding S. cerevisiae Vps34 × 1 Putative N-terminal domain of S. cerevisiae Vps30 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BECN1_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain D； PDBConstruct 1–557； UniProt 1–557

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	5dfz
Deposition date deposition_date	2015-08-27
Structure title title	Structure of Vps34 complex II from S. cerevisiae.
Keywords keywords	;Vps34, Vps15, Vps30, Vps38, Autophagy, vacuolar protein sorting, Yeast, Complex II, PI3P, kinase, lipid, WD40, BARA, C2, coiled-coil, HEAT, nanobody, transferase ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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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.

5dfz__assembly_1__model_1

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

Download this curve (.dat)

5dfz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dfz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	63.73 Å
Rg (electron density)	64.41 Å
Total Rg	64.27 Å
Atom count	14160
Residues	2853
Excluded volume	227780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dfz__assembly_1__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	Vacuolar protein sorting-associated protein 38
Molecular weight formula_weight	51072.9 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	14160

MKRFLLSRRQRHLRMICFHNISLFRANGDSKLIKEYGDGFIPCFFILESIRGELLYVSEVQSGSLRKLSFQELPKLTGASTMIVLKLVGLVPSDILCTISSDKNGIIDDKWCVLCTYTIDLNKLQPINEDTVLITGTNAPVLDLIDGSYTLAAEKIKPLKGLVSSHKRNISQVKIKFSLAYSSLLKLNKLLEYSSQVHEEINEISSKIEDDFLSLKNQNHWYMRTVQKSIETLEKEVLQRKKSKKNIEMAQLESNDTINHSKTELSLMSQDESINDDYGSIYSRFVQIKDRLDQLRFKKLYQLIGIFHSTDLFNSDRGYIYFEKPSSVNDVINRLKLKPLNIEILLRQAGESTKHREYVNSQLGYYLLFLHLTAIQIFKAPLPYRLMYYGSTSVIDSQYPLYFTDQMISKHQAKLIKAIHYFNADILQFKQILENYRPTGS

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Phosphatidylinositol 3-kinase VPS34
Molecular weight formula_weight	100973.1 kDa
EC 编号 ec_number	2.7.1.137
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MALNNITFCVSQDLDVPLKVKIKSLEGHKPLLKPSQKILNPELMLIGSNVFPSSDLIVSLQVFDKERNRNLTLPIYTPYIPFRNSRTWDYWLTLPIRIKQLTFSSHLRIILWEYNGSKQIPFFNLETSIFNLKDCTLKRGFESLKFRYDVIDHCEVVTDNKDQENLNKYFQGEFTRLPWLDEITISKLRKQRENRTWPQGTFVLNLEFPMLELPVVFIEREIMNTQMNIPTLKNNPGLSTGLREPNRNDPQIKISLGDKYHSTLKFYDPDQPNNDPIEEKYRRLERASKNANLDKQVKPDIKKRDYLNKIINYPPGTKLTAHEKGSIWKYRYYLMNNKKALTKLLQSTNLREESERVEVLELMDSWAEIDIDDALELLGSTFKNLSVRSYAVNRLKKASDKELELYLLQLVEAVCFENLSTFSDKSNSEFTIVDAVSSQKLSGDSMLLSTSHANQKLLKSISSESETSGTESLPIVISPLAEFLIRRALVNPRLGSFFYWYLKSESEDKPYLDQILSSFWSRLDKKSRNILNDQVRLINVLRECCETIKRLKDTTAKKMELLVHLLETKVRPLVKVRPIALPLDPDVLICDVCPETSKVFKSSLSPLKITFKTTLNQPYHLMFKVGDDLRQDQLVVQIISLMNELLKNENVDLKLTPYKILATGPQEGAIEFIPNDTLASILSKYHGILGYLKLHYPDENATLGVQGWVLDNFVKSCAGYCVITYILGVGDRHLDNLLVTPDGHFFHADFGYILGQDPKPFPPLMKLPPQIIEAFGGAESSNYDKFRSYCFVAYSILRRNAGLILNLFELMKTSNIPDIRIDPNGAILRVRERFNLNMSEEDATVHFQNLINDSVNALLPIVIDHLHNLAQYWRT

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	Serine/threonine-protein kinase VPS15
Molecular weight formula_weight	167082.5 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGAQLSLVVQASPSIAIFSYIDVLEEVHYVSQLNSSRFLKTCKALDPNGEIVIKVFIKPKDQYSLRPFLQRIRAQSFKLGQLPHVLNYSKLIETNRAGYMIRQHLKNNLYDRLSLRPYLQDIELKFIAFQLLNALKDIHNLNIVHGDIKTENILVTSWNWCILTDFAAFIKPVYLPEDNPGEFLFYFDTSKRRTCYLAPERFNSKLYQDGKSNNGRLTKEMDIFSLGCVIAEIFAEGRPIFNLSQLFKYKSNSYDVNREFLMEEMNSTDLRNLVLDMIQLDPSKRLSCDELLNKYRGIFFPDYFYTFIYDYFRNLVTMTTSTPISDNTCTNSTLEDNVKLLDETTEKIYRDFSQICHCLDFPLIKDGGEIGSDPPILESYKIEIEISRFLNTNLYFPQNYHLVLQQFTKVSEKIKSVKEECALLFISYLSHSIRSIVSTATKLKNLELLAVFAQFVSDENKIDRVVPYFVCCFEDSDQDVQALSLLTLIQVLTSVRKLNQLNENIFVDYLLPRLKRLLISNRQNTNYLRIVFANCLSDLAIIINRFQEFTFAQHCNDNSSTKYSAKLIQSVEDLTVSFLTDNDTYVKMALLQNILPLCKFFGRERTNDIILSHLITYLNDKDPALRVSLIQTISGISILLGTVTLEQYILPLLIQTITDSEELVVISVLQSLKSLFKTGLIRKKYYIDISKTTSPLLLHPNNWIRQFTLMIIIEIINKLSKAEVYCILYPIIRPFFEFDVEFNFKSMISCCKQPVSRSVYNLLCSWSVRASKSLFWKKIITNHVDSFGNNRIEFITKNYSSKNYGFNKRDTKSSSSLKGIKTSSTVYSHDNKEIPLTAEDRNWIDKFHIIGLTEKDIWKIVALRGYVIRTARVMAANPDFPYNNSNYRPLVQNSPPNLNLTNIMPRNIFFDVEFAEESTSEGQDSNLENQQIYKYDESEKDSNKLNINGSKQLSTVMDINGSLIFKNKSIATTTSNLKNVFVQLEPTSYHMHSPNHGLKDNANVKPERKVVVSNSYEGDVESIEKFLSTFKILPPLRDYKEFGPIQEIVRSPNMGNLRGKLIATLMENEPNSITSSAVSPGETPYLITGSDQGVIKIWNLKEIIVGEVYSSSLTYDCSSTVTQITMIPNFDAFAVSSKDGQIIVLKVNHYQQESEVKFLNCECIRKINLKNFGKNEYAVRMRAFVNEEKSLLVALTNLSRVIIFDIRTLERLQIIENSPRHGAVSSICIDEECCVLILGTTRGIIDIWDIRFNVLIRSWSFGDHAPITHVEVCQFYGKNSVIVVGGSSKTFLTIWNFVKGHCQYAFINSDEQPSMEHFLPIEKGLEELNFCGIRSLNALSTISVSNDKILLTDEATSSIVMFSLNELSSSKAVISPSRFSDVFIPTQVTANLTMLLRKMKRTSTHSVDDSLYHHDIINSISTCEVDETPLLVACDNSGLIGIFQGSSRPTTASENLYFQG

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 4 Entity 4 polymer

Description description	Nanobody binding S. cerevisiae Vps34
Molecular weight formula_weight	13772.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

QVQLQESGGGLVQPGGSLRLSCAPSGPFSPNSMGWYRQAPGKQRELVAVMTIDGRTNYQDSVKGRFTISRDYVKNTAYLQMNNLKPDDTAVYICNAETRGFMHWGQGTQVTVSSHHHHHHEPEA

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Vacuolar protein sorting-associated protein 30
Molecular weight formula_weight	63400.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MKCQTCHLPLQLDPSLEGLSLTQRNLLLSNNSIITATNENVISNKGIEAADNCGPQIPKERLRRLGEIQNIKDLNLIDDKLITDSFVFLNHDDDDNANITSNSREDQRYGNANGNDNKKANSDTSDGTSTFRDHDEEEQEATDEDENQQIQLNSKTLSTQVNAMTNVFNILSSQTNIDFPICQDCCNILINRLKSEYDDAIKERDTYAQFLSKLESQNKEISESNKEKQYSHNLSEKENLKKEEERLLDQLLRLEMTDDDLDGELVRLQEKKVQLENEKLQKLSDQNLMDLNNIQFNKNLQSLKLQYELSLNQLDKLRKINIFNATFKISHSGPFATINGLRLGSIPESVVPWKEINAALGQLILLLATINKNLKINLVDYELQPMGSFSKIKKRMVNSVEYNNSTTNAPGDWLILPVYYDENFNLGRIFRKETKFDKSLETTLEIISEITRQLSTIASSYSSQTLATSQDESSMNNANDVENSTSILELPYIMNKDKINGLSVKLHGSSPNLEWTTAMKFLLTNVKWLLAFSSNLLSKSITLSPTVNHNDKTISGNGS

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 6 Entity 6 polymer

Description description	Putative N-terminal domain of S. cerevisiae Vps30
Molecular weight formula_weight	4188.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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	Saccharomyces cerevisiae

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Unit-cell length a length_a	215.180 Å
Unit-cell length b length_b	226.840 Å
Unit-cell length c length_c	127.210 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	4.400 Å
Low-resolution limit resolution_low	50.358 Å
R factor r_factor	0.3687
R_work r_work	0.3683
R_free r_free	0.3762

Structure of Vps34 complex II from S. cerevisiae.

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

Vacuolar protein sorting-associated protein 38

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Phosphatidylinositol 3-kinase VPS34

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein kinase VPS15

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vacuolar protein sorting-associated protein 30

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

5dfz__assembly_1__model_1

5dfz__assembly_1__model_1 | I(q)

5dfz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

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

7. Citations (1)