SAXSdb — 8grf

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

Citrate synthase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	F-box protein UCC1 × 1 E3 ubiquitin ligase complex SCF subunit × 1 （A0A6A5Q435） 1,2-ETHANEDIOL × 10 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q445_YEASX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–460； UniProt 1–460 Author chain B； PDBConstruct 1–460； UniProt 1–460

E3 ubiquitin ligase complex SCF subunit

Saccharomyces cerevisiae

UniProt A0A6A5Q435

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Citrate synthase × 2 （A0A6A5Q445） F-box protein UCC1 × 1 1,2-ETHANEDIOL × 10 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q435_YEASX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–194； UniProt 1–194

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	8grf
Deposition date deposition_date	2022-09-01
Structure title title	Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate
Keywords keywords	F-box protein, glyoxylate cycle, E3 ubiquitin ligase, TRANSFERASE, TRANSFERASE-LIGASE complex; TRANSFERASE/LIGASE
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.

8grf__assembly_1__model_1

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

Download this curve (.dat)

8grf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8grf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.75 Å
Rg (electron density)	36.10 Å
Total Rg	36.64 Å
Atom count	10954
Residues	1362
Excluded volume	195730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8grf__assembly_1__model_1`	tetrameric （4）	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	Citrate synthase
Molecular weight formula_weight	51476.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11186

MTVPYLNSNRNVASYLQSNSSQEKTLKERFSEIYPIHAQDVRQFVKEHGKTKISDVLLEQVYGGMRGIPGSVWEGSVLDPEDGIRFRGRTIADIQKDLPKAKGSSQPLPEALFWLLLTGEVPTQAQVENLSADLMSRSELPSHVVQLLDNLPKDLHPMAQFSIAVTALESESKFAKAYAQGISKQDYWSYTFEDSLDLLGKLPVIAAKIYRNVFKDGKMGEVDPNADYAKNLVNLIGSKDEDFVDLMRLYLTIHSDHEGGNVSAHTSHLVGSALSSPYLSLASGLNGLAGPLHGRANQEVLEWLFALKEEVNDDYSKDTIEKYLWDTLNSGRVIPGYGHAVLRKTDPRYMAQRKFAMDHFPDYELFKLVSSIYEVAPGVLTEHGKTKNPWPNVDAHSGVLLQYYGLKESSFYTVLFGVSRAFGILAQLITDRAIGASIERPKSYSTEKYKELVKNIESKL

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	F-box protein UCC1
Molecular weight formula_weight	42828.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MNQSDSSLMDLPLEIHLSLLEYVPNELRAVNKYFYVLHNHSYKEKSLAWIAEDNYIWAVVKHSLCLYVKSLDPLRQHAREIIQETKEPGFNVPLCMTKYIADSWYIVYNALQYPGKIINMGWDKYTKSQDLNGSDSTSNFNSRPKERTLMQSLTALPVNFWSRKKDEPTPVNVWFYVKNAHVARYIPKIITEIGICNYGPKQIVASAGYINELITSEGIYCVNLGHLPRLYDEQIFEGTGTTHLPLELKAIDRTDSDVCINSDLVLLGYDFIPYQISKPWLLFRIEPVNSIEAIFNYSECSFSYQFAWSLACLQSEEKISFPRDTIIGHGLPYKPSKLIRIFVYKHPEQKQDLGQEIALPNWNTPYLRR

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	E3 ubiquitin ligase complex SCF subunit
Molecular weight formula_weight	22357.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MVTSNVVLVSGEGERFTVDKKIAERSLLLKNYLNDMHDSNLQNNSDSESDSDSETNHKSKDNNNGDDDDEDDDEIVMPVPNVRSSVLQKVIEWAEHHRDSNFPDEDDDDSRKSAPVDSWDREFLKVDQEMLYEIILAANYLNIKPLLDAGCKVVAEMIRGRSPEEIRRTFNIVNDFTPEEEAAIRRENEWAEDR

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 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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Unit-cell length a length_a	77.407 Å
Unit-cell length b length_b	150.976 Å
Unit-cell length c length_c	160.384 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.530 Å
Low-resolution limit resolution_low	36.640 Å
R factor r_factor	0.2164
R_work r_work	0.2153
R_free r_free	0.2477

Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate

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

Citrate synthase

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin ligase complex SCF subunit

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8grf__assembly_1__model_1

8grf__assembly_1__model_1 | I(q)

8grf__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 (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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate

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

Citrate synthase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E3 ubiquitin ligase complex SCF 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

8grf__assembly_1__model_1

8grf__assembly_1__model_1 | I(q)

8grf__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 (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 non-polymer

Entity 5 Entity 5 water

7. Citations (1)