SAXSdb — 7mex

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

Ubiquitin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ubiquitin-conjugating enzyme E2 2 × 1 （P06104） N-degron × 1 E3 ubiquitin-protein ligase UBR1 × 1 （P19812） ZINC ION × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–76； UniProt 1–76

Ubiquitin-conjugating enzyme E2 2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P06104

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ubiquitin × 1 （P0CG48） N-degron × 1 E3 ubiquitin-protein ligase UBR1 × 1 （P19812） ZINC ION × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBC2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–150； UniProt 3–152

E3 ubiquitin-protein ligase UBR1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P19812

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Ubiquitin × 1 （P0CG48） Ubiquitin-conjugating enzyme E2 2 × 1 （P06104） N-degron × 1 ZINC ION × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBR1_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–1950； UniProt 1–1950

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	7mex
Deposition date deposition_date	2021-04-08
Structure title title	Structure of yeast Ubr1 in complex with Ubc2 and N-degron
Keywords keywords	Ubiquitin E3 ligase, ubiquitination, Ubr1, Ubc2, Degron, N-end rule, TRANSFERASE; TRANSFERASE
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.

7mex__assembly_1__model_1

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

Download this curve (.dat)

7mex__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7mex__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.74 Å
Rg (electron density)	43.32 Å
Total Rg	43.54 Å
Atom count	15941
Residues	1967
Excluded volume	284880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7mex__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	Ubiquitin
Molecular weight formula_weight	8622.9 kDa
Mutation mutation	G76C
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	15941

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGC

Entity 2 Entity 2 polymer

Description description	Ubiquitin-conjugating enzyme E2 2
Molecular weight formula_weight	17203.4 kDa
EC 编号 ec_number	2.3.2.23
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TPARRRLMRDFKRMKEDAPPGVSASPLPDNVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKFLSEMFHPNVYANGEICLDILQNRWTPTYDVASILTSIQSLFNDPNPASPANVEAATLFKDHKSQYVKRVKETVEKSWEDD

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 S288C

Entity 3 Entity 3 polymer

Description description	N-degron
Molecular weight formula_weight	4571.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

RHGSGSGAWLLPVSLVKRKTTLAPNTQTASPPSYRALADSLMQ

Entity 4 Entity 4 polymer

Description description	E3 ubiquitin-protein ligase UBR1
Molecular weight formula_weight	225102.8 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MSVADDDLGSLQGHIRRTLRSIHNLPYFRYTRGPTERADMSRALKEFIYRYLYFVISNSGENLPTLFNAHPKQKLSNPELTVFPDSLEDAVDIDKITSQQTIPFYKIDESRIGDVHKHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEEQENDISEDPATNADIKEEDVWNDSVNIALVELVLAEVFDYFIDVFNQNIEPLPTIQKDITIKLREMTQQGKMYERAQFLNDLKYENDYMFDGTTTAKTSPSNSPEASPSLAKIDPENYTVIIYNDEYHNYSQATTALRQGVPDNVHIDLLTSRIDGEGRAMLKCSQDLSSVLGGFFAVQTNGLSATLTSWSEYLHQETCKYIILWITHCLNIPNSSFQTTFRNMMGKTLCSEYLNATECRDMTPVVEKYFSNKFDKNDPYRYIDLSILADGNQIPLGHHKILPESSTHSLSPLINDVETPTSRTYSNTRLQHILYFDNRYWKRLRKDIQNVIIPTLASSNLYKPIFCQQVVEIFNHITRSVAYMDREPQLTAIRECVVQLFTCPTNAKNIFENQSFLDIVWSIIDIFKEFCKVEGGVLIWQRVQKSNLTKSYSISFKQGLYTVETLLSKVHDPNIPLRPKEIISLLTLCKLFNGAWKIKRKEGEHVLHEDQNFISYLEYTTSIYSIIQTAEKVSEKSKDSIDSKLFLNAIRIISSFLGNRSLTYKLIYDSHEVIKFSVSHERVAFMNPLQTMLSFLIEKVSLKDAYEALEDCSDFLKISDFSLRSVVLCSQIDVGFWVRNGMSVLHQASYYKNNPELGSYSRDIHLNQLAILWERDDIPRIIYNILDRWELLDWFTGEVDYQHTVYEDKISFIIQQFIAFIYQILTERQYFKTFSSLKDRRMDQIKNSIIYNLYMKPLSYSKLLRSVPDYLTEDTTEFDEALEEVSVFVEPKGLADNGVFKLKASLYAKVDPLKLLNLENEFESSATIIKSHLAKDKDEIAKVVLIPQVSIKQLDKDALNLGAFTRNTVFAKVVYKLLQVCLDMEDSTFLNELLHLVHGIFRDDELINGKDSIPEAYLSKPICNLLLSIANAKSDVFSESIVRKADYLLEKMIMKKPNELFESLIASFGNQYVNDYKDKKLRQGVNLQETEKERKRRLAKKHQARLLAKFNNQQTKFMKEHESEFDEQDNDVDMVGEKVYESEDFTCALCQDSSSTDFFVIPAYHDHSPIFRPGNIFNPNEFMPMWDGFYNDDEKQAYIDDDVLEALKENGSCGSRKVFVSCNHHIHHNCFKRYVQKKRFSSNAFICPLCQTFSNCTLPLCQTSKANTGLSLDMFLESELSLDTLSRLFKPFTEENYRTINSIFSLMISQCQGFDKAVRKRANFSHKDVSLILSVHWANTISMLEIASRLEKPYSISFFRSREQKYKTLKNILVCIMLFTFVIGKPSMEFEPYPQQPDTVWNQNQLFQYIVRSALFSPVSLRQTVTEALTTFSRQFLRDFLQGLSDAEQVTKLYAKASKIGDVLKVSEQMLFALRTISDVRMEGLDSESIIYDLAYTFLLKSLLPTIRRCLVFIKVLHELVKDSENETLVINGHEVEEELEFEDTAEFVNKALKMITEKESLVDLLTTQESIVSHPYLENIPYEYCGIIKLIDLSKYLNTYVTQSKEIKLREERSQHMKNADNRLDFKICLTCGVKVHLRADRHEMTKHLNKNCFKPFGAFLMPNSSEVCLHLTQPPSNIFISAPYLNSHGEVGRNAMRRGDLTTLNLKRYEHLNRLWINNEIPGYISRVMGDEFRVTILSNGFLFAFNREPRPRRIPPTDEDDEDMEEGEDGFFTEGNDEMDVDDETGQAANLFGVGAEGIAGGGVRDFFQFFENFRNTLQPQGNGDDDAPQNPPPILQFLGPQFDGATIIRNTNPRNLDEDDSDDNDDSDEREIW

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 S288C

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	7

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7mexA01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	7mexC01
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	3.35 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	232915

Structure of yeast Ubr1 in complex with Ubc2 and N-degron

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

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-conjugating enzyme E2 2

State in the Current Structure

Other States of the Same Protein in the Database

E3 ubiquitin-protein ligase UBR1

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

7mex__assembly_1__model_1

7mex__assembly_1__model_1 | I(q)

7mex__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of yeast Ubr1 in complex with Ubc2 and N-degron

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

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

Ubiquitin-conjugating enzyme E2 2

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-protein ligase UBR1

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

7mex__assembly_1__model_1

7mex__assembly_1__model_1 | I(q)

7mex__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)