SAXSdb — 6yjd

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

Capsid assembly scaffolding protein,Prelamin-A/C

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	NICKEL (II) ION × 4 CHLORIDE ION × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LMNA_HUMAN
Isoform	P02545-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 50–127； UniProt 326–403

Capsid assembly scaffolding protein,Prelamin-A/C

Homo sapiens

UniProt P13848

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	NICKEL (II) ION × 4 CHLORIDE ION × 2 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCAF_BPPH2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–49； UniProt 1–48

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	6yjd
Deposition date deposition_date	2020-04-03
Structure title title	Lamin A coil2 dimer stabilized by N-terminal capping
Keywords keywords	intermediate filaments, lamin, coiled-coil, NUCLEAR PROTEIN; NUCLEAR PROTEIN
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.

6yjd__assembly_1__model_1

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

Download this curve (.dat)

6yjd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6yjd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.13 Å
Rg (electron density)	36.85 Å
Total Rg	35.99 Å
Atom count	1684
Residues	208
Excluded volume	29666 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6yjd__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	Capsid assembly scaffolding protein,Prelamin-A/C
Molecular weight formula_weight	14894.8 kDa
Mutation mutation	F40C
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	844

GMPLKPEEHEDILNKLLDPELAQSERTEALQQLRVNYGSCVSEYNDLTKSLARERDTSRRLLAEKEREMAEMRARMQQQLDEYQELLDIKLALDMEIHAYRKLLEGEEERLRLSPSPTSQRSRGRAS

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 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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Unit-cell length a length_a	117.250 Å
Unit-cell length b length_b	117.250 Å
Unit-cell length c length_c	93.156 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	hexagonal

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	44.620 Å
R factor r_factor	—
R_work r_work	0.2533
R_free r_free	0.3042

Lamin A coil2 dimer stabilized by N-terminal capping

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

Capsid assembly scaffolding protein,Prelamin-A/C

State in the Current Structure

Other States of the Same Protein in the Database

Capsid assembly scaffolding protein,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

6yjd__assembly_1__model_1

6yjd__assembly_1__model_1 | I(q)

6yjd__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Lamin A coil2 dimer stabilized by N-terminal capping

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

Capsid assembly scaffolding protein,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

Capsid assembly scaffolding protein,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

6yjd__assembly_1__model_1

6yjd__assembly_1__model_1 | I(q)

6yjd__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)