6K5A: H/Cl exchange transporter ClcA

Crystal structure of the E148D/R147A/F317A mutant in presence of 200 mM NaBr. Determined by X-ray diffraction at 3.16 Å resolution. Released 28 Aug 2019.

Method: X-ray diffraction
Resolution: 3.16 Å
Organisms: Escherichia coli MS 117-3, Mus musculus
Chains: 6
Atoms: 13,175
Mol. weight: 194.57 kDa
Released: 28 Aug 2019

Explore 6K5A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K5A contains 68 α-helices and 95 β-strands across 6 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: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-26	9
α-helix	33-70	38
α-helix	75-98	24
α-helix	102-104	3
α-helix	109-117	9
α-helix	124-140	17
β-strand	146	1	1
α-helix	148-166	19
α-helix	171-190	20
α-helix	193-199	7
α-helix	200-204	5
α-helix	215-230	16
α-helix	249-284	36
α-helix	288-308	21
α-helix	310-312	3
α-helix	319-324	6
α-helix	330-349	20
β-strand	355	1	1
α-helix	357-376	20
α-helix	386-394	9
α-helix	397-400	4
α-helix	405-416	12
α-helix	419-421	3
α-helix	422-438	17
α-helix	446-455	10

Chain B: 25 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-26	9
α-helix	33-70	38
α-helix	75-98	24
α-helix	102-104	3
α-helix	109-116	8
α-helix	124-139	16
β-strand	146	1	2
α-helix	148-165	18
α-helix	172-190	19
α-helix	193-199	7
α-helix	200-204	5
α-helix	215-231	17
α-helix	249-251	3
α-helix	254-284	31
α-helix	288-308	21
α-helix	317-319	3
α-helix	321-324	4
α-helix	330-348	19
β-strand	355	1	2
α-helix	358-378	21
α-helix	380-382	3
α-helix	386-394	9
α-helix	397-400	4
α-helix	405-416	12
α-helix	419-421	3
α-helix	422-437	16
α-helix	444-454	11

Chain C: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	11-12	2	4
β-strand	17-25	9	3
β-strand	33-39	7	5
α-helix	44	1
β-strand	45-51	7	5
β-strand	58-60	3	5
β-strand	68-73	6	3
α-helix	74-76	3
β-strand	78-84	7	3
β-strand	92-100	9	5
β-strand	107-111	5	5
β-strand	115-117	3	5
β-strand	118-119	2	4
α-helix	122-124	3
β-strand	125	1	6
α-helix	126-127	2
β-strand	128-131	4	7
β-strand	143-145	3	8
β-strand	148-153	6	7
β-strand	154	1	6
β-strand	159-162	4	9
α-helix	163-165	3
β-strand	171-173	3	7
α-helix	174-176	3
β-strand	177-179	3	7
β-strand	182-189	8	7
β-strand	190-192	3	8
β-strand	202-207	6	9
α-helix	208-210	3
β-strand	212-217	6	9

Chain D: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	10
β-strand	10-13	4	11
β-strand	19-25	7	10
β-strand	32-37	6	11
β-strand	44-47	4	11
β-strand	48	1	12
β-strand	52	1	12
β-strand	63-66	4	10
β-strand	69-74	6	10
β-strand	84-89	6	11
β-strand	96-97	2	11
β-strand	98	1	10
β-strand	102-105	4	11
β-strand	110	1	13
β-strand	113	1	14
β-strand	116-117	2	14
α-helix	121-126	6
β-strand	128-136	9	14
β-strand	139	1	13
β-strand	144-149	6	15
β-strand	153-154	2	15
β-strand	158-162	5	14
α-helix	163-164	2
β-strand	173-181	9	14
α-helix	182-186	5
β-strand	190-196	7	15
β-strand	204-209	6	15

Chain E: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	11-12	2	17
β-strand	17-25	9	16
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	58-60	3	18
β-strand	68-73	6	16
α-helix	74-76	3
β-strand	78-84	7	16
β-strand	92-101	10	18
β-strand	106-111	6	18
β-strand	115-117	3	18
β-strand	118-119	2	17
β-strand	125	1	19
β-strand	128-132	5	20
β-strand	143-153	11	20
β-strand	154	1	19
β-strand	159-162	4	21
β-strand	171-173	3	20
α-helix	174-176	3
β-strand	177-179	3	20
β-strand	182-192	11	20
α-helix	195-198	4
β-strand	202-207	6	21
α-helix	208-210	3
β-strand	212-217	6	21

Chain F: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	22
β-strand	10-13	4	23
β-strand	18-25	8	22
β-strand	33-37	5	23
β-strand	44-48	5	23
β-strand	52-53	2	23
β-strand	61-66	6	22
β-strand	69-75	7	22
α-helix	79-81	3
β-strand	84-89	6	23
α-helix	95	1
β-strand	96-97	2	23
β-strand	101-105	5	23
β-strand	110	1	24
β-strand	113-117	5	25
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	25
β-strand	139	1	24
β-strand	144-149	6	26
β-strand	154	1	26
β-strand	158-162	5	25
α-helix	163-166	4
β-strand	172-181	10	25
α-helix	182-186	5
β-strand	190-197	8	26
β-strand	200-209	10	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H(+)/Cl(-) exchange transporter ClcA	A, B	protein	473	Escherichia coli MS 117-3	P37019 (AlphaFold model)
Fab fragment, heavy chain	C, E	protein	222	Mus musculus	P01808 (AlphaFold model)
Fab fragment, light chain	D, F	protein	211	Mus musculus	P01837 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6K5A_1 H(+)/Cl(-) exchange transporter ClcA (chains A, B)
MKTDTPSLETPQAARLRRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWL
QNQRMGALVHTADNYPLLLTVAFLCSAVLAMFGYFLVRKYAPEAGGSGIPEIEGALEDQR
PVRWWRVLPVKFFGGLGTLGGGMVLGADGPTVQIGGNIGRMVLDIFRLKGDEARHTLLAT
GAAAGLAAAFNAPLAGILFIIEEMRPQFRYTLISIKAVFIGVIMSTIMYRIFNHEVALID
VGKLSDAPLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGG
LCGLLGFVAPATSGGGANLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPM
LALGTVLGTAFGMVAVELFPQYHLEAGTFAIAGMGALLAASIRAPLTGIILVLEMTDNYQ
LILPMIITGLGATLLAQFTGGKPLYSAILARTLAKQEAEQLARSKAASASENT

Sequence of entity 2 (C, E), FASTA

>6K5A_2 Fab fragment, heavy chain (chains C, E)
EVRLLESGGGLVQPGGSLKLSCAASGFDYSRYWMSWVRQAPGKGLKWIGEINPVSSTINY
TPSLKDKFIISRDNAKDTLYLQISKVRSEDTALYYCARLYYGYGYWYFDVWGAGTTVTVS
SAKTTPPSVYPLAPGSAAAAASMVTLGCLVKGYFPEPVTVTWNSGSLAAGVHTFPAVLQA
ALYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRA

Sequence of entity 3 (D, F), FASTA

>6K5A_3 Fab fragment, light chain (chains D, F)
DIVLTQSPAIMSAAPGDKVTMTCSASSSVSYIHWYQQKSGTSPKRWIYDTSKLTSGVPVR
FSGSGSGTSYSLTINTMEAEDAATYYCQQWSSHPQTFGGGTKLEILRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRA

Primary citation

Mutation of external glutamate residue reveals a new intermediate transport state and anion binding site in a CLC Cl-/H+antiporter. Park, K., Lee, B.C., Lim, H.H. Proc Natl Acad Sci U S A (2019) 116:17345-17354. DOI 10.1073/pnas.1901822116 · PubMed

Other PDB entries of the same protein (UniProt P37019 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ENE 2.4 Å, Structure of the N- and C-terminal trimmed ClC-ec1 Cl-/H+ antiporter and Fab Complex
1OTS 2.51 Å, Structure of the Escherichia coli ClC Chloride channel and Fab Complex
8GA1 2.6 Å, CLC-ec1 R230C/L249C/C85A at pH 4.5 100mM Cl Swap
8GA5 2.6 Å, CLC-ec1 L25C/A450C/C85A at pH 4.5 100mM Cl Intermediate
6V2J 2.62 Å, Crystal structure of ClC-ec1 triple mutant (E113Q, E148Q, E203Q)
6ADB 2.69 Å, Crystal structure of the E148N mutant CLC-ec1 in 20mM bromide
3DET 2.8 Å, Structure of the E148A, Y445A doubly ungated mutant of E.coli CLC_Ec1, Cl-/H+ antiporter
4KKL 2.85 Å, Structure of the E148A mutant of CLC-ec1 delta NC construct in 100mM fluoride
4KK8 2.86 Å, Structure of the E148Q mutant of CLC-ec1 deltaNC construct in 100mM fluoride
4KJQ 2.88 Å, Structure of the CLC-ec1 deltaNC construct in 100mM fluoride
3EJZ 2.9 Å, Structure of E203V mutant E.coli Cl-/H+ exchanger, CLC-ec1
7CVT 2.9 Å, Crystal structure of the C85A/L194A/H234C mutant CLC-ec1 with Fab fragment

Browse structure collections

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