SAXSdb — 3brd

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

Lin-12 and glp-1 phenotype protein 1, isoform a

Caenorhabditis elegans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	;DNA (5'-D(DTPDTPDAPDCPDTPDGPDTPDGPDGPDGPDAPDAPDAPDGPDA)-3') ; × 1 ;DNA (5'-D(DAPDAPDTPDCPDTPDTPDTPDCPDCPDCPDAPDCPDAPDGPDT)-3') ; × 1 Protein lin-12 × 1 （P14585） 1,2-ETHANEDIOL × 10 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9TYY1_CAEEL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 6–477； UniProt 192–663

Protein lin-12

Caenorhabditis elegans

UniProt P14585

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	;DNA (5'-D(DTPDTPDAPDCPDTPDGPDTPDGPDGPDGPDAPDAPDAPDGPDA)-3') ; × 1 ;DNA (5'-D(DAPDAPDTPDCPDTPDTPDTPDCPDCPDCPDAPDCPDAPDGPDT)-3') ; × 1 Lin-12 and glp-1 phenotype protein 1, isoform a × 1 （Q9TYY1） 1,2-ETHANEDIOL × 10 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LIN12_CAEEL
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–29； UniProt 930–957

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	3brd
Deposition date deposition_date	2007-12-21
Structure title title	CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, P212121
Keywords keywords	;protein-DNA complex, signaling, transcription, Notch, DNA-binding, ANK repeat, Developmental protein, Differentiation, EGF-like domain, Glycoprotein, Membrane, Transmembrane, DNA BINDING PROTEIN-DNA COMPLEX ;; DNA BINDING PROTEIN/DNA
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.

3brd__assembly_1__model_1

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

Download this curve (.dat)

3brd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3brd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.79 Å
Rg (electron density)	26.37 Å
Total Rg	27.23 Å
Atom count	4176
Residues	472
Excluded volume	72443 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3brd__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 (6)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(DTPDTPDAPDCPDTPDGPDTPDGPDGPDGPDAPDAPDAPDGP*DA)-3') ;
Molecular weight formula_weight	4673.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	4328

TTACTGTGGGAAAGA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DAPDAPDTPDCPDTPDTPDTPDCPDCPDCPDAPDCPDAPDGP*DT)-3') ;
Molecular weight formula_weight	4503.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

AATCTTTCCCACAGT

Entity 3 Entity 3 polymer

Description description	Lin-12 and glp-1 phenotype protein 1, isoform a
Molecular weight formula_weight	53761.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GPLGSGDSVQSLTSDRMIDFLSNKEKYECVISIFHAKVAQKSYGNEKRFFCPPPCIYLIGQGWKLKKDRVAQLYKTLKASAQKDAAIENDPIHEQQATELVAYIGIGSDTSERQQLDFSTGKVRHPGDQRQDPNIYDYCAAKTLYISDSDKRKYFDLNAQFFYGCGMEIGGFVSQRIKVISKPSKKKQSMKNTDCKYLCIASGTKVALFNRLRSQTVSTRYLHVEGNAFHASSTKWGAFTIHLFDDERGLQETDNFAVRDGFVYYGSVVKLVDSVTGIALPRLRIRKVDKQQVILDASCSEEPVSQLHKCAFQMIDNELVYLCLSHDKIIQHQATAINEHRHQINDGAAWTIISTDKAEYRFFEAMGQVANPISPCPVVGSLEVDGHGEASRVELHGRDFKPNLKVWFGATPVETTFRSEESLHCSIPPVSQVRNEQTHWMFTNRTTGDVEVPISLVRDDGVVYSSGLTFSYKSLER

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Protein lin-12
Molecular weight formula_weight	3522.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

SPGNRTRKRRMINASVWMPPMENEEKNRK

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 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 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	131

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3brda1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain

Domain ID domain_id	d3brda2
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.8 — DNA-binding protein LAG-1 (CSL)

Domain ID domain_id	d3brda3
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.7 — DNA-binding protein LAG-1 (CSL)
Family Family family	b.42.7.1 — DNA-binding protein LAG-1 (CSL)

CATH v4.4 (3 domains)

Domain ID domain_id	3brdA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1450 — LAG1, DNA binding domain

Domain ID domain_id	3brdA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3brdA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	60.153 Å
Unit-cell length b length_b	98.866 Å
Unit-cell length c length_c	126.313 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	4

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

Resolution resolution	2.210 Å
Low-resolution limit resolution_low	39.870 Å
R factor r_factor	0.2110
R_work r_work	0.2080
R_free r_free	0.2570

CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, P212121

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

Lin-12 and glp-1 phenotype protein 1, isoform a

State in the Current Structure

Other States of the Same Protein in the Database

Protein lin-12

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

3brd__assembly_1__model_1

3brd__assembly_1__model_1 | I(q)

3brd__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

CSL (Lag-1) bound to DNA with Lin-12 RAM peptide, P212121

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

Lin-12 and glp-1 phenotype protein 1, isoform a

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 lin-12

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

3brd__assembly_1__model_1

3brd__assembly_1__model_1 | I(q)

3brd__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)