4K07: PDB entry 4K07

Crystal structure of the amyloid-forming immunoglobulin AL-103 cis-proline 95 mutant. Determined by X-ray diffraction at 2.83 Å resolution. Released 30 Oct 2013.

Method: X-ray diffraction
Resolution: 2.83 Å
Organism: Homo sapiens
Chains: 10
Atoms: 8,476
Mol. weight: 140.58 kDa
Released: 30 Oct 2013

Explore 4K07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4K07 contains 46 α-helices and 110 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, F and G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	97	1
β-strand	98	1	2
α-helix	99	1
β-strand	102-106	5	2

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	3
β-strand	10-13	4	4
β-strand	19-25	7	3
β-strand	33-38	6	4
β-strand	45-49	5	4
β-strand	53-54	2	4
α-helix	55	1
β-strand	62-67	6	3
β-strand	70-75	6	3
α-helix	80-82	3
β-strand	84-90	7	4
α-helix	96	1
β-strand	97-98	2	4
β-strand	102-106	5	4

Chains C, D, E, H, I and J: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	5
β-strand	10-13	4	4
β-strand	19-25	7	5
β-strand	33-38	6	4
β-strand	45-49	5	4
β-strand	53-54	2	4
α-helix	55	1
β-strand	62-67	6	5
β-strand	70-75	6	5
α-helix	80-82	3
β-strand	84-90	7	4
α-helix	97	1
β-strand	98	1	4
α-helix	99	1
β-strand	102-106	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Amyloidogenic immunoglobulin light chain protein AL-103	A, B, C, D, E, F, G, H, I, J	protein	129	Homo sapiens	P01594 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>4K07_1 Amyloidogenic immunoglobulin light chain protein AL-103 (chains A, B, C, D, E, F, G, H, I, J)
MRAKLLGIVLTTPIAISSFASTDIQMTQSPSSLSASVGDRVTITCQASQDISNYLIWYQQ
KPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYHNLPYTF
GPGTKLEIK

Primary citation

Kinetic control in protein folding for light chain amyloidosis and the differential effects of somatic mutations. Blancas-Mejia, L.M., Tischer, A., Thompson, J.R. et al. J Mol Biol (2014) 426:347-361. DOI 10.1016/j.jmb.2013.10.016 · PubMed

Other PDB entries of the same protein (UniProt P01594 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2Q20 1.3 Å, Structure of the germline Vk1 O18/O8 light chain variable domain homodimer
3CDC 1.53 Å, kI O18/O8 N34I/Y87H immunoglobulin light chain variable domain
3CDF 1.53 Å, kI O18/O8 Y87H immunoglobulin light chain variable domain
1B0W 1.8 Å, Structural comparison of amyloidogenic light chain dimer in two crystal forms with…
1QP1 2.06 Å, Kappa variable light chain
1JV5 2.2 Å, Anti-blood group A Fv
3CDY 2.43 Å, AL-09 H87Y, immunoglobulin light chain variable domain
7CZQ 2.8 Å, S protein of SARS-CoV-2 in complex bound with P2B-1A10
7CZV 3.3 Å, S protein of SARS-CoV-2 in complex bound with P5A-1B6_3B
7CZU 3.4 Å, S protein of SARS-CoV-2 in complex bound with P5A-1B6_2B

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