4KML: Major prion protein

Probing the N-terminal beta-sheet conversion in the crystal structure of the full-length human prion protein bound to a Nanobody. Determined by X-ray diffraction at 1.5 Å resolution. Released 19 Feb 2014.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Homo sapiens, Lama glama
Chains: 2
Atoms: 1,920
Mol. weight: 40.48 kDa
Released: 19 Feb 2014

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

Secondary structure: helices and β-sheets

4KML contains 11 α-helices and 14 β-strands across 2 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.

Chain A: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	118-122	5	1
β-strand	125-130	6	1
α-helix	136-138	3
α-helix	144-153	10
α-helix	154-156	3
β-strand	162-163	2	1
α-helix	166-168	3
α-helix	172-193	22
α-helix	200-224	25

Chain B: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	2
β-strand	10-12	3	3
β-strand	18-24	7	2
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	2
β-strand	78-83	6	2
α-helix	88-90	3
β-strand	92-99	8	3
α-helix	100	1
α-helix	108-110	3
β-strand	111-112	2	3
β-strand	118-122	5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major prion protein	A	protein	241	Homo sapiens	P04156 (AlphaFold model)
Nanobody	B	protein	130	Lama glama

Sequence of entity 1 (A), FASTA

>4KML_1 Major prion protein (chains A)
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGKRPKPGGWNTGGSRYPGQGSPGGNRYP
PQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMK
HMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYS
NQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGS
S

Sequence of entity 2 (B), FASTA

>4KML_2 Nanobody (chains B)
AVQLQESGGGLVQPGGSLRLSCAASGRTFSSYNMGWFRQAPGKGREFVASITSSGDKSDY
TDSVKGRFTISRDNAKNTMYLQMNNLKPEDTATYYCARGLGIYIIRARGGYDHWGQGTQV
TVSSHHHHHH

Primary citation

Probing the N-Terminal beta-Sheet Conversion in the Crystal Structure of the Human Prion Protein Bound to a Nanobody. Abskharon, R.N., Giachin, G., Wohlkonig, A. et al. J Am Chem Soc (2014) 136:937-944. DOI 10.1021/ja407527p · PubMed

Other PDB entries of the same protein (UniProt P04156 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OL9 0.85 Å, Peptide corresponding to residues 170-175 of human prion
7RVE 0.85 Å, Segment from the S170N mutant of the human prion protein 168-176 EYNNQNNFV
7RVJ 1.0 Å, Segment from the human prion protein 169-175 YSNQNNF
7RVK 1.0 Å, Segment from Y169G mutant of the human prion protein 169-175 GSNQNNF
7RVL 1.0 Å, Segment from the Y169F mutant of the human prion protein 168-176 EFSNQNNFV
7RVC 1.0 Å, Segment from the human prion protein 168-176 EYSNQNNFV
3MD4 1.15 Å, Prion peptide
3MD5 1.4 Å, Prion peptide
4E1H 1.4 Å, Fragment of human prion protein
6PQA 1.46 Å, GAVVGG segment 119-124 from human prion
4N9O 1.5 Å, Probing the N-terminal beta-sheet conversion in the crystal structure of the human prion…
6PQ5 1.5 Å, AGAAAA segment 113-118 from human prion

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