6QBA: Retinol-Binding Protein 4

Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold. Determined by X-ray diffraction at 1.8 Å resolution. Released 3 Jun 2020.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, Sulfolobus solfataricus
Chains: 2
Atoms: 2,182
Mol. weight: 29.28 kDa
Ligands: ZN, 2T1
Released: 3 Jun 2020

Explore 6QBA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QBA contains 4 α-helices and 18 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: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
α-helix	6-8	3
β-strand	22-30	9	2
β-strand	42-47	6	2
β-strand	53-64	12	2
β-strand	67-79	13	2
β-strand	85-92	8	2
β-strand	99-109	11	2
β-strand	114-118	5	2
β-strand	119-123	5	3
β-strand	128	1	1
β-strand	129-133	5	3
β-strand	134-138	5	2
α-helix	146-158	13
β-strand	166-167	2	2

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-14	5	4
α-helix	16-18	3
β-strand	21-25	5	4
β-strand	28-32	5	4
β-strand	43-46	4	4
α-helix	52-60	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinol-binding protein 4	A	protein	185	Homo sapiens	P02753 (AlphaFold model)
DNA-binding protein 7a	B	protein	61	Sulfolobus solfataricus	P61991 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6QBA_1 Retinol-binding protein 4 (chains A)
GPERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAK
GRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQY
SCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYCDGRS
ERNLL

Sequence of entity 2 (B), FASTA

>6QBA_2 DNA-binding protein 7a (chains B)
ATVKLTYQGEEKQVDISKIKRVARYGQNIYFSYDEGGGAYDYGAVSEKDAPKELLQMLEK
Q

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
2T1	2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid	C20 H19 F3 N2 O3	1

Water and common crystallization additives (ACT, PEG, IMD) are not listed.

Primary citation

A conformation-specific ON-switch for controlling CAR T cells with an orally available drug. Zajc, C.U., Dobersberger, M., Schaffner, I. et al. Proc Natl Acad Sci U S A (2020) 117:14926-14935. DOI 10.1073/pnas.1911154117 · PubMed

Other PDB entries of the same protein (UniProt P02753 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NU2 1.5 Å, Structure of non-fluorescent human urine RBP4
5NU7 1.5 Å, Structure of human holo plasma RBP4
5NU9 1.5 Å, Structure of human amniotic fluid RBP4 saturated with palmitate
5NU8 1.59 Å, Structure of human urine RBP4 saturated with palmitate
5NUA 1.6 Å, Structure of human urine RBP4 saturated with laurate
5NUB 1.6 Å, Structure of human amniotic fluid RBP4 saturated with laurate
2WQ9 1.65 Å, Crystal Structure of RBP4 bound to Oleic Acid
5NU6 1.68 Å, Structure of non-fluorescent human amniotic fluid RBP4
1JYD 1.7 Å, Crystal Structure of Recombinant Human Serum Retinol-Binding Protein at 1.7 A Resolution
2WR6 1.8 Å, Structure of the complex of RBP4 with linoleic acid
1JYJ 2.0 Å, Crystal Structure of a Double Variant (W67L/W91H) of Recombinant Human Serum…
1RBP 2.0 Å, Crystallographic refinement of human serum retinol binding protein at 2 Å resolution

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