1YFP: Yellow-emission variant of GFP

Structure of yellow-emission variant of GFP. Determined by X-ray diffraction at 2.5 Å resolution. Released 28 Oct 1998.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Aequorea victoria
Chains: 2
Atoms: 3,494
Mol. weight: 51.42 kDa
Released: 28 Oct 1998

Explore 1YFP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YFP contains 12 α-helices and 28 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.

Chains A and B: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	12-22	11	1
β-strand	25-36	12	1
β-strand	41-48	8	1
α-helix	57-60	4
α-helix	69-71	3
β-strand	73	1	1
α-helix	76-81	6
α-helix	83-86	4
β-strand	92-100	9	1
β-strand	105-115	11	1
β-strand	118-128	11	1
β-strand	141	1	2
β-strand	148-155	8	1
β-strand	160-170	11	1
β-strand	171	1	2
β-strand	176-187	12	1
α-helix	194-197	4
β-strand	199-208	10	1
β-strand	217-227	11	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Yellow fluorescent protein	A, B	protein	225	Aequorea victoria	P42212 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1YFP_1 YELLOW FLUORESCENT PROTEIN (chains A, B)
KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVT
TFXLQCFARYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIE
LKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQ
NTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGI

Primary citation

Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein. Wachter, R.M., Elsliger, M.A., Kallio, K. et al. Structure (1998) 6:1267-1277. DOI 10.1016/S0969-2126(98)00127-0 · PubMed

Other PDB entries of the same protein (UniProt P42212 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6L27 0.77 Å, X-ray crystal structure of the mutant green fluorescent protein
6JGJ 0.78 Å, Crystal structure of the F99S/M153T/V163A/E222Q variant of GFP at 0.78 A
6KL0 0.8 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 7.0
6JGI 0.85 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of GFP at 0.85 A
6KL1 0.85 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of non-deuterated GFP at pD 8.5
2WUR 0.9 Å, Atomic resolution structure of GFP measured on a rotating anode
6KKZ 0.9 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 8.5
6JGH 0.94 Å, Crystal structure of the F99S/M153T/V163A/T203I variant of GFP at 0.94 A
4AS8 1.02 Å, X-ray structure of the cyan fluorescent protein Cerulean cryoprotected with ethylene…
5OXC 1.02 Å, Structure of Cerulean Fluorescent Protein at 1.02 Angstrom resolution
7PCA 1.05 Å, Functional and structural characterization of redox sensitive superfolder green…
4GF6 1.1 Å, crystal structure of GFP with cuprum bound at the Incorporated metal Chelating Amino…

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1YFP is part of these collections:

Fluorescent and glowing proteins

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