3VHT: GFP-Wrnip1 UBZ domain fusion protein

Crystal structure of GFP-Wrnip1 UBZ domain fusion protein in complex with ubiquitin. Determined by X-ray diffraction at 2.4 Å resolution. Released 10 Oct 2012.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Aequorea victoria, Homo sapiens, Mus musculus
Chains: 3
Atoms: 4,631
Mol. weight: 65.49 kDa
Ligands: ZN
Released: 10 Oct 2012

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

Secondary structure: helices and β-sheets

3VHT contains 20 α-helices and 37 β-strands across 3 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	11-22	12	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
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

Chain B: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
β-strand	12-22	11	3
β-strand	25-36	12	3
β-strand	41-48	8	3
α-helix	57-60	4
α-helix	69-71	3
β-strand	73	1	3
α-helix	74-75	2
α-helix	76-81	6
α-helix	83-86	4
β-strand	92-100	9	3
β-strand	105-115	11	3
β-strand	118-128	11	3
β-strand	141	1	4
β-strand	148-155	8	3
α-helix	156-158	3
β-strand	160-170	11	3
β-strand	171	1	4
β-strand	176-187	12	3
α-helix	194-197	4
β-strand	199-208	10	3
β-strand	217-227	11	3
β-strand	241-243	3	5
β-strand	250-252	3	5
α-helix	253-255	3
α-helix	256-266	11

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	6
β-strand	48-49	2	6
α-helix	50-51	2
β-strand	55	1	7
β-strand	66-71	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Green fluorescent protein	A	protein	233	Aequorea victoria	P42212 (AlphaFold model)
Green fluorescent protein,ATPase WRNIP1	B	protein	271	Aequorea victoria, Homo sapiens	P42212 (AlphaFold model), Q96S55 (AlphaFold model)
Ubiquitin	C	protein	76	Mus musculus	P62983 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VHT_1 Green fluorescent protein (chains A)
GSHMSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPW
PTLVTTFXVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTL
VNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLA
DHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITGS

Sequence of entity 2 (B), FASTA

>3VHT_2 Green fluorescent protein,ATPase WRNIP1 (chains B)
GSHMSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPW
PTLVTTFXVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTL
VNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLA
DHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITGSDPFLSQL
HQVQCPVCQQMMPAAHINSHLDRCLLLHPAG

Sequence of entity 3 (C), FASTA

>3VHT_3 Ubiquitin (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

A novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1. Suzuki, N., Rohaim, A., Kato, R. et al. FEBS J (2016). DOI 10.1111/febs.13734 · 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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