SAXSdb — 8dat

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

Cell division control protein 48

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Nuclear protein localization protein 4 × 1 （P33755） Ubiquitin fusion degradation protein 1 × 1 （P53044） Ubiquitin × 3 （P0CG63） ADENOSINE-5'-TRIPHOSPHATE × 5 ADENOSINE-5'-DIPHOSPHATE × 7 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDC48_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–838； UniProt 1–835 Author chain B； PDBConstruct 4–838； UniProt 1–835 Author chain C； PDBConstruct 4–838； UniProt 1–835 Author chain D； PDBConstruct 4–838； UniProt 1–835 Author chain E； PDBConstruct 4–838； UniProt 1–835 Author chain F； PDBConstruct 4–838； UniProt 1–835

Nuclear protein localization protein 4

Saccharomyces cerevisiae

UniProt P33755

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cell division control protein 48 × 6 （P25694） Ubiquitin fusion degradation protein 1 × 1 （P53044） Ubiquitin × 3 （P0CG63） ADENOSINE-5'-TRIPHOSPHATE × 5 ADENOSINE-5'-DIPHOSPHATE × 7 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NPL4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 4–583； UniProt 1–580

Ubiquitin fusion degradation protein 1

Saccharomyces cerevisiae

UniProt P53044

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cell division control protein 48 × 6 （P25694） Nuclear protein localization protein 4 × 1 （P33755） Ubiquitin × 3 （P0CG63） ADENOSINE-5'-TRIPHOSPHATE × 5 ADENOSINE-5'-DIPHOSPHATE × 7 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UFD1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 3–363； UniProt 1–361

Ubiquitin

Saccharomyces cerevisiae

UniProt P0CG63

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Cell division control protein 48 × 6 （P25694） Nuclear protein localization protein 4 × 1 （P33755） Ubiquitin fusion degradation protein 1 × 1 （P53044） ADENOSINE-5'-TRIPHOSPHATE × 5 ADENOSINE-5'-DIPHOSPHATE × 7 ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBI4P_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain J； PDBConstruct 1–76； UniProt 1–76 Author chain K； PDBConstruct 1–76； UniProt 1–76 Author chain L； PDBConstruct 1–76； UniProt 1–76

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	8dat
Deposition date deposition_date	2022-06-14
Structure title title	Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB)
Keywords keywords	ATPASE, ATPASE COMPLEX, UBIQUITIN, SUMO, SMT3, QUALITY CONTROL, MOTOR PROTEIN; MOTOR 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.

8dat__assembly_1__model_1

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

Download this curve (.dat)

8dat__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dat__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.64 Å
Rg (electron density)	54.49 Å
Total Rg	54.54 Å
Atom count	34635
Residues	4388
Excluded volume	615150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dat__assembly_1__model_1`	undecameric （11）	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 (7)

Entity 1 Entity 1 polymer

Description description	Cell division control protein 48
Molecular weight formula_weight	92389.2 kDa
EC 编号 ec_number	3.6.4.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	34635

GSHMGEEHKPLLDASGVDPREEDKTATAILRRKKKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLIVLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIADTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEPEEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIAKARGGSLGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVKVEGEDVEMTDEGAKAEQEPEVDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKASRGQFSNFNFNDAPLGTTATDNANSNNSAPSGAGAAFGSNAEEDDDLYS

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nuclear protein localization protein 4
Molecular weight formula_weight	66144.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GSHMLIRFRSKNGTHRVSCQENDLFGTVIEKLVGNLDPNADVDTFTVCEKPGQGIHAVSELADRTVMDLGLKHGDMLILNYSDKPANEKDGVNVEIGSVGIDSKGIRQHRYGPLRIKELAVDEELEKEDGLIPRQKSKLCKHGDRGMCEYCSPLPPWDKEYHEKNKIKHISFHSYLKKLNENANKKENGSSYISPLSEPDFRINKRCHNGHEPWPRGICSKCQPSAITLQQQEFRMVDHVEFQKSEIINEFIQAWRYTGMQRFGYMYGSYSKYDNTPLGIKAVVEAIYEPPQHDEQDGLTMDVEQVKNEMLQIDRQAQEMGLSRIGLIFTDLSDAGAGDGSVFCKRHKDSFFLSSLEVIMAARHQTRHPNVSKYSEQGFFSSKFVTCVISGNLEGEIDISSYQVSTEAEALVTADMISGSTFPSMAYINDTTDERYVPEIFYMKSNEYGITVKENAKPAFPVDYLLVTLTHGFPNTDTETNSKFVSSTGFPWSNRQAMGQSQDYQELKKYLFNVASSGDFNLLHEKISNFHLLLYINSLQILSPDEWKLLIESAVKNEWEESLLKLVSSAGWQTLVMILQESG

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	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin fusion degradation protein 1
Molecular weight formula_weight	40001.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GSMFSGFSSFGGGNGFVNMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPPVGYVEPDYKALKAQQDKEKKNSFGKGQVLDPSVLGQGSMSTRIDYAGIANSSRNKLSKFVGQGQNISGKAPKAEPKQDIKDMKITFDGEPAKLDLPEGQLFFGFPMVLPKEDEESAAGSKSSEQNFQGQGISLRKSNKRKTKSDHDSSKSKAPKSPEVIEID

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	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8568.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K,L

MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

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	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	7

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

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	8datJ01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	8datK01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	8datL01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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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	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	22510

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB)

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

Cell division control protein 48

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nuclear protein localization protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin fusion degradation protein 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

Ubiquitin

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

8dat__assembly_1__model_1

8dat__assembly_1__model_1 | I(q)

8dat__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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)