6ghd

Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases

Method: X-RAY DIFFRACTION

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

Emerin

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Barrier-to-autointegration factor × 2 （O75531） Prelamin-A/C × 1 （P02545） SULFATE ION × 5 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Barrier-to-autointegration factor × 2 （O75531） Prelamin-A/C × 1 （P02545） SULFATE ION × 3 1,2-ETHANEDIOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EMD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain G； PDBConstruct 2–45； UniProt 2–45 Author chain H； PDBConstruct 2–45； UniProt 2–45

Barrier-to-autointegration factor

Homo sapiens

UniProt O75531

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Emerin × 1 （P50402） Prelamin-A/C × 1 （P02545） SULFATE ION × 5 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Emerin × 1 （P50402） Prelamin-A/C × 1 （P02545） SULFATE ION × 3 1,2-ETHANEDIOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BAF_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–88； UniProt 2–89 Author chain C； PDBConstruct 1–88； UniProt 2–89 Author chain D； PDBConstruct 1–88； UniProt 2–89 Author chain E； PDBConstruct 1–88； UniProt 2–89

Prelamin-A/C

Homo sapiens

UniProt P02545

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Emerin × 1 （P50402） Barrier-to-autointegration factor × 2 （O75531） SULFATE ION × 5 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Emerin × 1 （P50402） Barrier-to-autointegration factor × 2 （O75531） SULFATE ION × 3 1,2-ETHANEDIOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LMNA_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–119； UniProt 428–546 Author chain F； PDBConstruct 1–119； UniProt 428–546

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	6ghd
Deposition date deposition_date	2018-05-07
Structure title title	Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases
Keywords keywords	nuclear envelope, gene expression, ternary 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.

6ghd__assembly_1__model_1

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

Download this curve (.dat)

6ghd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ghd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.65 Å
Rg (electron density)	22.60 Å
Total Rg	23.46 Å
Atom count	2707
Residues	339
Excluded volume	47697 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ghd__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ghd__assembly_2__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	Emerin
Molecular weight formula_weight	5324.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H
Atom count atom_count	5674

GDNYADLSDTELTTLLRRYNIPHGPVVGSTRRLYEKKIFEYETQR

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	Barrier-to-autointegration factor
Molecular weight formula_weight	9814.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,A,C

TTSQKHRDFVAEPMGEKPVGSLAGIGEVLGKKLEERGFDKAYVVLGQFLVLKKDEDLFREWLKDTAGANAKQSRDAFGALREWADAFL

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	Prelamin-A/C
Molecular weight formula_weight	13206.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SSFSQHARTSGRVAVEEVDEEGKFVRLRNKSNEDQSMGNWQIKRQNGDDPLLTYRFPPKFTLKAGQVVTIWAAGAGATHSPPTDLVWKAQNTWGCGNSLRTALINSTGEEVAMRKLVRS

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

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	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	280

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d6ghda_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.5 — Barrier-to-autointegration factor, BAF
Family Family family	a.60.5.1 — Barrier-to-autointegration factor, BAF

Domain ID domain_id	d6ghdb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.16 — Lamin A/C globular tail domain
Family Family family	b.1.16.1 — Lamin A/C globular tail domain

Domain ID domain_id	d6ghdc_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.5 — Barrier-to-autointegration factor, BAF
Family Family family	a.60.5.1 — Barrier-to-autointegration factor, BAF

Domain ID domain_id	d6ghdd_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.5 — Barrier-to-autointegration factor, BAF
Family Family family	a.60.5.1 — Barrier-to-autointegration factor, BAF

Domain ID domain_id	d6ghde_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.5 — Barrier-to-autointegration factor, BAF
Family Family family	a.60.5.1 — Barrier-to-autointegration factor, BAF

Domain ID domain_id	d6ghdf_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.16 — Lamin A/C globular tail domain
Family Family family	b.1.16.1 — Lamin A/C globular tail domain

Domain ID domain_id	d6ghdg1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.1 — LEM domain
Family Family family	a.140.1.1 — LEM domain

Domain ID domain_id	d6ghdg2
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	d6ghdh_
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.1 — LEM domain
Family Family family	a.140.1.1 — LEM domain

CATH v4.4 (8 domains)

Domain ID domain_id	6ghdA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	40 — Barrier-to-autointegration factor, BAF

Domain ID domain_id	6ghdB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1260 — Lamin Tail domain

Domain ID domain_id	6ghdC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	40 — Barrier-to-autointegration factor, BAF

Domain ID domain_id	6ghdD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	40 — Barrier-to-autointegration factor, BAF

Domain ID domain_id	6ghdE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	40 — Barrier-to-autointegration factor, BAF

Domain ID domain_id	6ghdF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1260 — Lamin Tail domain

Domain ID domain_id	6ghdG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6ghdH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	57.770 Å
Unit-cell length b length_b	62.750 Å
Unit-cell length c length_c	64.340 Å
Unit-cell angle α angle_alpha	66.44 °
Unit-cell angle β angle_beta	66.55 °
Unit-cell angle γ angle_gamma	88.05 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	49.152 Å
R factor r_factor	0.1944
R_work r_work	0.1917
R_free r_free	0.2468

Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases

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

Emerin

State in the Current Structure

Other States of the Same Protein in the Database

Barrier-to-autointegration factor

State in the Current Structure

Other States of the Same Protein in the Database

Prelamin-A/C

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

6ghd__assembly_1__model_1

6ghd__assembly_1__model_1 | I(q)

6ghd__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

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

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases

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

Emerin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Barrier-to-autointegration factor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Prelamin-A/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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ghd__assembly_1__model_1

6ghd__assembly_1__model_1 | I(q)

6ghd__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

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

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. Citations (1)