4xl1

Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF1)

Method: X-RAY DIFFRACTION

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

Neurogenic locus notch homolog protein 1

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	Delta-like protein × 1 （D3ZHH1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-glucopyranose × 3 alpha-L-fucopyranose × 1 CALCIUM ION × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 1	Delta-like protein × 1 （D3ZHH1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-glucopyranose × 3 alpha-L-fucopyranose × 1 CALCIUM ION × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count
3	Other combination	Heteromer	Protein 4 其他Polymer 2	Delta-like protein × 2 （D3ZHH1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-glucopyranose × 6 alpha-L-fucopyranose × 2 CALCIUM ION × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOTC1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–116； UniProt 412–526 Author chain D； PDBConstruct 2–116； UniProt 412–526

Delta-like protein

Rattus norvegicus

UniProt D3ZHH1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	Neurogenic locus notch homolog protein 1 × 1 （Q07008） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-glucopyranose × 3 alpha-L-fucopyranose × 1 CALCIUM ION × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 1	Neurogenic locus notch homolog protein 1 × 1 （Q07008） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-glucopyranose × 3 alpha-L-fucopyranose × 1 CALCIUM ION × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count
3	Other combination	Heteromer	Protein 4 其他Polymer 2	Neurogenic locus notch homolog protein 1 × 2 （Q07008） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-glucopyranose × 6 alpha-L-fucopyranose × 2 CALCIUM ION × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3ZHH1_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–228； UniProt 27–252 Author chain E； PDBConstruct 3–228； UniProt 27–252

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	4xl1
Deposition date deposition_date	2015-01-13
Structure title title	Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF1)
Keywords keywords	glycosylation, EGF domains, receptor-ligand complex, PROTEIN BINDING; PROTEIN BINDING
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.

4xl1__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4xl1__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4xl1__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	36.28 Å
Rg (electron density)	36.64 Å
Total Rg	36.68 Å
Atom count	5507
Residues	676
Excluded volume	96417 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4xl1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4xl1__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4xl1__assembly_3__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 (8)

Entity 1 Entity 1 polymer

Description description	Neurogenic locus notch homolog protein 1
Molecular weight formula_weight	12734.3 kDa
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	5865

PDVDECALGANPCEHAGKCLNTLGSFECQCLQGYTGPRCEIDVNECISNPCQNDATCLDQIGEFQCICMPGYEGVYCEINTDECASSPCLHNGRCVDKINEFLCQCPKGFSGHLCQSG

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Delta-like protein
Molecular weight formula_weight	25754.8 kDa
Mutation mutation	G28S, F107L, L206P
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GSSSIFQLRLQEFANERGMLANGRPCEPGCRTFFRICLKHYQATFSEGPCTFGNVSTPVLGTNSFVIRDKNSGSGRNPLQLPLNFTWPGTFSLNIQAWHTPGDDLRPETSPGNSLISQIIIQGSLAVGKNWKSDEQNNTLTRLRYSYRVVCSDNYYGDSCSRLCKKRDDHFGHYECQPDGSPSCLPGWTGKYCDQPICLSGCHEQNGYCSKPDECNCRPGWQGPLCNEAA

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	alpha-L-fucopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	325

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d4xl1a1
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d4xl1a2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d4xl1a3
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d4xl1a4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4xl1d1
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d4xl1d2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d4xl1d3
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.0 — automated matches

Domain ID domain_id	d4xl1d4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4xl1d5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	4xl1A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	4xl1A02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	4xl1A03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	4xl1B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3510 —

Domain ID domain_id	4xl1D01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	4xl1D02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	4xl1D03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	4xl1E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3510 —

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Unit-cell length a length_a	77.809 Å
Unit-cell length b length_b	93.700 Å
Unit-cell length c length_c	99.126 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	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	49.560 Å
R factor r_factor	0.2200
R_work r_work	0.2180
R_free r_free	0.2590

Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF1)

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

Neurogenic locus notch homolog protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Delta-like protein

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

4xl1__assembly_3__model_1

4xl1__assembly_3__model_1 | I(q)

4xl1__assembly_3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF1)

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

Neurogenic locus notch homolog 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

Delta-like protein

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

4xl1__assembly_3__model_1

4xl1__assembly_3__model_1 | I(q)

4xl1__assembly_3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)