3OGO: GFP:GFP-nanobody complex

Structure of the GFP:GFP-nanobody complex at 2.8 A resolution in spacegroup P21212. Determined by X-ray diffraction at 2.8 Å resolution. Released 25 Aug 2010.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Aequorea victoria, CAMELUS DROMEDARIUS
Chains: 8
Atoms: 11,212
Mol. weight: 167.8 kDa
Ligands: IPA
Released: 25 Aug 2010

Explore 3OGO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3OGO contains 35 α-helices and 106 β-strands across 8 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: 8 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
α-helix	37-39	3
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	149-155	7	1
α-helix	156-158	3
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

Chains C and D: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	12-22	11	5
β-strand	25-36	12	5
β-strand	41-48	8	5
α-helix	57-60	4
α-helix	69-71	3
β-strand	73	1	5
α-helix	76-81	6
α-helix	83-86	4
β-strand	92-100	9	5
β-strand	105-115	11	5
β-strand	118-128	11	5
β-strand	141	1	6
β-strand	149-155	7	5
α-helix	156-158	3
β-strand	160-170	11	5
β-strand	171	1	6
β-strand	176-187	12	5
α-helix	196-197	2
β-strand	199-208	10	5
β-strand	217-227	11	5

Chains E and F: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	9
β-strand	12-13	2	10
β-strand	19-26	8	9
β-strand	35-40	6	11
β-strand	47-52	6	11
β-strand	59-61	3	11
β-strand	69-74	6	9
β-strand	79-84	6	9
α-helix	89-91	3
β-strand	93-101	9	11
β-strand	103-106	4	11
β-strand	110-112	3	11
β-strand	113-114	2	10

Chain G: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	15
β-strand	12-13	2	16
β-strand	19-26	8	15
β-strand	35-40	6	17
β-strand	47-52	6	17
β-strand	59-61	3	17
α-helix	63-65	3
β-strand	66	1	15
β-strand	69-74	6	15
β-strand	79-84	6	15
α-helix	89-91	3
β-strand	93-101	9	17
β-strand	103-106	4	17
β-strand	110-112	3	17
β-strand	113-114	2	16

Chain H: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	18
β-strand	12-13	2	19
β-strand	19-26	8	18
β-strand	35-40	6	20
β-strand	47-52	6	20
β-strand	59-61	3	20
β-strand	66	1	18
β-strand	69-74	6	18
β-strand	79-84	6	18
α-helix	89-91	3
β-strand	93-101	9	20
β-strand	103-106	4	20
β-strand	110-112	3	20
β-strand	113-114	2	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Green fluorescent protein	A, B, C, D	protein	247	Aequorea victoria	P42212 (AlphaFold model)
GFP-nanobody	E, F, G, H	protein	123	CAMELUS DROMEDARIUS

Sequence of entity 1 (A, B, C, D), FASTA

>3OGO_1 Green fluorescent protein (chains A, B, C, D)
MAHHHHHHSSGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICT
TGKLPVPWPTLVTTLXVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAE
VKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNI
EDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITL
GMDELYK

Sequence of entity 2 (E, F, G, H), FASTA

>3OGO_2 GFP-nanobody (chains E, F, G, H)
MQVQLVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSS
YEDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVSSKHHH
HHH

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	3

Primary citation

Structural and thermodynamic analysis of the GFP:GFP-nanobody complex. Kubala, M.H., Kovtun, O., Alexandrov, K. et al. Protein Sci (2010) 19:2389-2401. DOI 10.1002/pro.519 · 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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3OGO is part of these collections:

Fluorescent and glowing proteins

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