SAXSdb — 9hne

▼

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

Eukaryotic peptide chain release factor GTP-binding subunit ERF3A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） ZINC ION × 1 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） ZINC ION × 1 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ERF3A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–197； UniProt 300–496 Author chain D； PDBConstruct 1–197； UniProt 300–496

DNA damage-binding protein 1

Homo sapiens

UniProt Q16531

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A × 1 （P15170） Protein cereblon × 1 （Q96SW2） ZINC ION × 1 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A × 1 （P15170） Protein cereblon × 1 （Q96SW2） ZINC ION × 1 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDB1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1140； UniProt 1–1140 Author chain E； PDBConstruct 1–1140； UniProt 1–1140

Protein cereblon

Homo sapiens

UniProt Q96SW2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A × 1 （P15170） DNA damage-binding protein 1 × 1 （Q16531） ZINC ION × 1 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A × 1 （P15170） DNA damage-binding protein 1 × 1 （Q16531） ZINC ION × 1 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CRBN_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–404； UniProt 40–442 Author chain F； PDBConstruct 2–404； UniProt 40–442

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	9hne
Deposition date deposition_date	2024-12-10
Last revision last_revision	2025-10-22
Structure title title	Cereblon in complex with DDB1, GSPT1 and Compound-1
Keywords keywords	CRBN, GSPT1, TPD, Molecular glue, ONCOPROTEIN; ONCOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

9hne__assembly_1__model_1

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

Download this curve (.dat)

9hne__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9hne__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.70 Å
Rg (electron density)	46.26 Å
Total Rg	46.36 Å
Atom count	13023
Residues	1647
Excluded volume	233180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9hne__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9hne__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
Molecular weight formula_weight	21851.7 kDa
EC 编号 ec_number	3.6.5.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	26021

GPIRLPIVDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDTVAPGENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVP

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	DNA damage-binding protein 1
Molecular weight formula_weight	127097.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	unidentified baculovirus

Entity 3 Entity 3 polymer

Description description	Protein cereblon
Molecular weight formula_weight	46408.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

SEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	unidentified baculovirus

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid
Molecular weight formula_weight	306.2 kDa
Source method src_method	syn
Copy count entity_count	2

▶

Unit-cell length a length_a	158.340 Å
Unit-cell length b length_b	112.380 Å
Unit-cell length c length_c	177.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	49.490 Å
R factor r_factor	0.2625
R_work r_work	0.2595
R_free r_free	0.3356

Cereblon in complex with DDB1, GSPT1 and Compound-1

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

Eukaryotic peptide chain release factor GTP-binding subunit ERF3A

State in the Current Structure

Other States of the Same Protein in the Database

DNA damage-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Protein cereblon

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

9hne__assembly_1__model_1

9hne__assembly_1__model_1 | I(q)

9hne__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 non-polymer

7. Citations (1)

Cereblon in complex with DDB1, GSPT1 and Compound-1

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

Eukaryotic peptide chain release factor GTP-binding subunit ERF3A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA damage-binding 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

Protein cereblon

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

9hne__assembly_1__model_1

9hne__assembly_1__model_1 | I(q)

9hne__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 non-polymer

7. Citations (1)