5H3D: PDB entry 5H3D

Helical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by cryo-electron microscopy and MD simulation. Determined by electron microscopy at 14.0 Å resolution. Released 16 Jan 2019.

Method: Electron microscopy
Resolution: 14.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,616
Mol. weight: 173.34 kDa
Released: 16 Jan 2019

Explore 5H3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H3D contains 48 α-helices and 36 β-strands across 4 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: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	15-68	54
α-helix	72	1
α-helix	74-104	31
α-helix	105-110	6
α-helix	111-115	5
α-helix	118-143	26
α-helix	149-208	60
α-helix	210-248	39
α-helix	254-257	4
β-strand	260	1	1
β-strand	267	1	1
β-strand	268-275	8	2
β-strand	284-291	8	2
β-strand	294-298	5	2
α-helix	304-305	2
β-strand	306-309	4	2
β-strand	316-319	4	2
β-strand	328-332	5	2
β-strand	338-341	4	2
α-helix	345-363	19

Chain B: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
α-helix	15-67	53
α-helix	71-72	2
α-helix	74	1
α-helix	75-80	6
α-helix	81-104	24
α-helix	105-110	6
α-helix	111-115	5
α-helix	118-142	25
α-helix	150-244	95
α-helix	245-249	5
β-strand	260-262	3	3
β-strand	265-267	3	3
β-strand	268-275	8	4
β-strand	283-290	8	4
β-strand	295-297	3	4
α-helix	304-305	2
β-strand	306-309	4	4
α-helix	312-314	3
β-strand	315-318	4	4
β-strand	328-333	6	4
β-strand	337-341	5	4
α-helix	345-359	15

Chain C: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	15-69	55
α-helix	74-105	32
α-helix	106-110	5
α-helix	111-115	5
α-helix	118-142	25
α-helix	149-208	60
α-helix	210-248	39
α-helix	254-257	4
β-strand	260	1	5
α-helix	262-265	4
β-strand	267	1	5
β-strand	268-275	8	6
β-strand	284-291	8	6
β-strand	294-298	5	6
β-strand	306-309	4	6
β-strand	315-319	5	6
β-strand	328-333	6	6
β-strand	338-341	4	6
α-helix	345-363	19

Chain D: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	15-69	55
α-helix	74	1
α-helix	75-80	6
α-helix	81-105	25
α-helix	106-110	5
α-helix	111-115	5
α-helix	118-140	23
α-helix	150-244	95
α-helix	245-249	5
β-strand	260	1	7
β-strand	267	1	7
β-strand	268-275	8	8
β-strand	283-291	9	8
β-strand	294-298	5	8
β-strand	305-309	5	8
β-strand	316-318	3	8
β-strand	328-332	5	8
β-strand	337-341	5	8
α-helix	345-359	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1	A, B, C, D	protein	382	Homo sapiens	Q15027 (AlphaFold model)

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

>5H3D_1 Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1 (chains A, B, C, D)
GPLGSMTVKLDFEECLKDSPRFRASIELVEAEVSELETRLEKLLKLGTGLLESGRHYLAA
SRAFVVGICDLARLGPPEPMMAECLEKFTVSLNHKLDSHAELLDATQHTLQQQIQTLVKE
GLRGFREARRDFWRGAESLEAALTHNAEVPRRRAQEAEEAGAALRTARAGYRGRALDYAL
QINVIEDKRKFDIMEFVLRLVEAQATHFQQGHEELSRLSQYRKELGAQLHQLVLNSAREK
RDMEQRHVLLKQKELGGEEPEPSLREGPGGLVMEGHLFKRASNAFKTWSRRWFTIQSNQL
VYQKKYKDPVTVVVDDLRLCTVKLCPDSERRFCFEVVSTSKSCLLQADSERLLQLWVSAV
QSSIASAFSQARLDDSPRGPGQ

Primary citation

ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages. Chan, C., Pang, X., Zhang, Y. et al. PLoS Comput Biol (2019) 15:e1007081-e1007081. DOI 10.1371/journal.pcbi.1007081 · PubMed

Other PDB entries of the same protein (UniProt Q15027 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NSW 2.2 Å, Crystal structure of the BAR-PH domain of ACAP1
3JUE 2.3 Å, Crystal Structure of ArfGAP and ANK repeat domain of ACAP1
3T9K 2.3 Å, Crystal Structure of ACAP1 C-portion mutant S554D fused with integrin beta1 peptide
4F1P 2.3 Å, Crystal Structure of mutant S554D for ArfGAP and ANK repeat domain of ACAP1
4CKG 15.0 Å, Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane tubules by…
4CKH 17.0 Å, Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane tubules by…

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