9bj9

Human CRL-2 ZYG11B binding to human NLRP1 Gly/N degron

Method: ELECTRON MICROSCOPY

▼

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

Protein zyg-11 homolog B

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Cullin-2 × 1 （Q13617） Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus × 1 （Q9C000） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZY11B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–748； UniProt 2–744

Elongin-B

Homo sapiens

UniProt Q15370

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein zyg-11 homolog B × 1 （Q9C0D3） Elongin-C × 1 （Q15369） Cullin-2 × 1 （Q13617） Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus × 1 （Q9C000） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 1–118

Elongin-C

Homo sapiens

UniProt Q15369

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein zyg-11 homolog B × 1 （Q9C0D3） Elongin-B × 1 （Q15370） Cullin-2 × 1 （Q13617） Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus × 1 （Q9C000） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELOC_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–96； UniProt 17–112

Cullin-2

Homo sapiens

UniProt Q13617

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein zyg-11 homolog B × 1 （Q9C0D3） Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus × 1 （Q9C000） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CUL2_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–745； UniProt 1–745

Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus

Homo sapiens

UniProt Q9C000

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein zyg-11 homolog B × 1 （Q9C0D3） Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Cullin-2 × 1 （Q13617） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NLRP1_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain P； PDBConstruct 1–9； UniProt 131–139

E3 ubiquitin-protein ligase RBX1

Homo sapiens

UniProt P62877

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein zyg-11 homolog B × 1 （Q9C0D3） Elongin-B × 1 （Q15370） Elongin-C × 1 （Q15369） Cullin-2 × 1 （Q13617） Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus × 1 （Q9C000） ZINC ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBX1_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain R； PDBConstruct 1–108； UniProt 1–108

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9bj9
Deposition date deposition_date	2024-04-25
Structure title title	Human CRL-2 ZYG11B binding to human NLRP1 Gly/N degron
Keywords keywords	Gly/N degron, Cullin E3 ligase, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9bj9__assembly_1__model_1

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

Download this curve (.dat)

9bj9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9bj9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.00 Å
Rg (electron density)	53.71 Å
Total Rg	53.83 Å
Atom count	14204
Residues	1767
Excluded volume	253810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9bj9__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Protein zyg-11 homolog B
Molecular weight formula_weight	84463.3 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	14204

SHMVDPEDQAGAAMEEASPYSLLDICLNFLTTHLEKFCSARQDGTLCLQEPGVFPQEVADRLLRTMAFHGLLNDGTVGIFRGNQMRLKRACIRKAKISAVAFRKAFCHHKLVELDATGVNADITITDIISGLGSNKWIQQNLQCLVLNSLTLSLEDPYERCFSRLSGLRALSITNVLFYNEDLAEVASLPRLESLDISNTSITDITALLACKDRLKSLTMHHLKCLKMTTTQILDVVRELKHLNHLDISDDKQFTSDIALRLLEQKDILPNLVSLDVSGRKHVTDKAVEAFIQQRPSMQFVGLLATDAGYSEFLTGEGHLKVSGEANETQIAEALKRYSERAFFVREALFHLFSLTHVMEKTKPEILKLVVTGMRNHPMNLPVQLAASACVFNLTKQDLAAGMPVRLLADVTHLLLKAMEHFPNHQQLQKNCLLSLCSDRILQDVPFNRFEAAKLVMQWLCNHEDQNMQRMAVAIISILAAKLSTEQTAQLGTELFIVRQLLQIVKQKTNQNSVDTTLKFTLSALWNLTDESPTTCRHFIENQGLELFMRVLESFPTESSIQQKVLGLLNNIAEVQELHSELMWKDFIDHISSLLHSVEVEVSYFAAGIIAHLISRGEQAWTLSRSQRNSLLDDLHSAILKWPTPECEMVAYRSFNPFFPLLGCFTTPGVQLWAVWAMQHVCSKNPSRYCSMLIEEGGLQHLYNIKDHEHTDPHVQQIAVAILDSLEKHIVRHGRPPPCKKQPQARLN

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Elongin-B
Molecular weight formula_weight	13147.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Elongin-C
Molecular weight formula_weight	10843.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Cullin-2
Molecular weight formula_weight	90428.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTEADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKKCIEVLIDKQYIERSQASADEYSYVALEGGGGWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 5 Entity 5 polymer

Description description	Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus
Molecular weight formula_weight	2124.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

GSERRVLRQXXXXXXXXXXXX

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	E3 ubiquitin-protein ligase RBX1
Molecular weight formula_weight	12290.0 kDa
EC 编号 ec_number	2.3.2.27,2.3.2.32
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

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	3

▶

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	triclinic

Resolution resolution	4.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	80380

Human CRL-2 ZYG11B binding to human NLRP1 Gly/N degron

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

Protein zyg-11 homolog B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongin-C

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cullin-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

Peptide from NACHT, LRR and PYD domains-containing protein 1, N-terminus

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 RBX1

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

9bj9__assembly_1__model_1

9bj9__assembly_1__model_1 | I(q)

9bj9__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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

7. Citations (2)