3UDC: Membrane protein

Name: PDB 3UDC: Crystal structure of a membrane protein
Published: 2012-10-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Crystal structure of a membrane protein. Determined by X-ray diffraction at 3.35 Å resolution. Released 31 Oct 2012.

Method: X-ray diffraction
Resolution: 3.35 Å
Organisms: Thermoanaerobacter tengcongensis, Escherichia coli
Chains: 7
Atoms: 14,903
Mol. weight: 227.24 kDa
Released: 31 Oct 2012

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

Secondary structure: helices and β-sheets

3UDC contains 49 α-helices and 70 β-strands across 7 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, E and F: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-50	34
α-helix	60-87	28
α-helix	92-109	18
α-helix	111-125	15
β-strand	134-137	4	1
β-strand	140-147	8	1
β-strand	151-156	6	1
β-strand	160-165	6	1
α-helix	166-168	3
β-strand	172-174	3	1
β-strand	180-189	10	2
α-helix	194-211	18
β-strand	215	1	2
β-strand	220-228	9	2
β-strand	231-240	10	2
α-helix	245-262	18
β-strand	273-278	6	3

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-50	34
α-helix	60-87	28
α-helix	92-109	18
α-helix	111-125	15
β-strand	134-137	4	1
β-strand	140-147	8	1
β-strand	151-156	6	1
β-strand	160-165	6	1
α-helix	166-168	3
β-strand	172-174	3	1
β-strand	180-189	10	4
α-helix	194-211	18
β-strand	215	1	4
β-strand	220-228	9	4
β-strand	231-240	10	4
α-helix	245-262	18
β-strand	271-278	8	3

Chains C, D and G: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-47	31
α-helix	60-87	28
α-helix	92-109	18
α-helix	111-125	15
β-strand	134-137	4	1
β-strand	140-147	8	1
β-strand	151-156	6	1
β-strand	160-165	6	1
α-helix	166-168	3
β-strand	172-174	3	1
β-strand	180-189	10	5
α-helix	194-211	18
β-strand	215	1	5
β-strand	220-228	9	5
β-strand	231-240	10	5
α-helix	245-262	18
β-strand	273-278	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance…	A, B, C, D, E, F, G	protein	285	Thermoanaerobacter tengcongensis, Escherichia coli	P0C0S1 (AlphaFold model), Q8R6L9 (AlphaFold model)

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

>3UDC_1 Small-conductance mechanosensitive channel, C-terminal peptide from Small-conductance mechanosensitive channel (chains A, B, C, D, E, F, G)
MWADIYHKLVEIYDIKAVKFLLDVLKILIIAFIGIKFADFLIYRFYKLYSKSKIQLPQRK
IDTLTSLTKNAVRYIIYFLAGASILKLFNIDMTSLLAVAGIGSLAIGFGAQNLVKDMISG
FFIIFEDQFSVGDYVTINGISGTVEEIGLRVTKIRGFSDGLHIIPNGEIKMVTNLTKDSM
MAVVNIAFPIDEDVDKIIEGLQEICEEVKKSRDDLIEGPTVLGITDMQDSKLVIMVYAKT
QPMQKWAVERDIRYRVKKMFDQKNISFPYPQMDVNFKRVKEDKAA

Primary citation

Structure and molecular mechanism of an anion-selective mechanosensitive channel of small conductance. Zhang, X., Wang, J., Feng, Y. et al. Proc Natl Acad Sci U S A (2012) 109:18180-18185. DOI 10.1073/pnas.1207977109 · PubMed

Other PDB entries of the same protein (UniProt P0C0S1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ONJ 2.3 Å, Mechanosensitive channel MscS solubilized with LMNG in open conformation
9E68 2.5 Å, Cryo-EM structure of MscS/YnaI chimera in DOPC nanodiscs
7OOA 2.7 Å, Mechanosensitive channel MscS solubilized with LMNG in open conformation with added lipid
9H2S 2.7 Å, a YnaI-MscS chimera in a closed conformation purified in DDM with additional lipids…
9H2V 2.8 Å, a YnaI-MscS chimera in an open conformation purified in DDM showing ligand-filled pockets
6RLD 2.9 Å, Structure of the mechanosensitive channel mscs embedded in the membrane bilayer
5AJI 2.99 Å, MscS D67R1 high resolution
6PWN 3.1 Å, MscS Nanodisc with N-terminal His-Tag
7OO0 3.1 Å, Mechanosensitive channel MscS solubilized with DDM in open conformation
7OO6 3.1 Å, Mechanosensitive channel MscS solubilized with DDM in closed conformation with added lipid
8DDJ 3.1 Å, Open MscS in PC14.1 Nanodiscs
6VYK 3.2 Å, Cryo-EM structure of mechanosensitive channel MscS in PC-18:1 nanodiscs

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