4KK8: H/Cl exchange transporter ClcA

Structure of the E148Q mutant of CLC-ec1 deltaNC construct in 100mM fluoride. Determined by X-ray diffraction at 2.86 Å resolution. Released 21 Aug 2013.

Method: X-ray diffraction
Resolution: 2.86 Å
Organisms: Escherichia coli, Mus musculus
Chains: 6
Atoms: 13,227
Mol. weight: 189.1 kDa
Ligands: F
Released: 21 Aug 2013

Explore 4KK8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KK8 contains 78 α-helices and 94 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: 26 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	18-27	10
α-helix	33-70	38
α-helix	75-100	26
α-helix	102-104	3
β-strand	106	1	1
α-helix	109-116	8
α-helix	124-140	17
β-strand	146	1	2
α-helix	148-166	19
α-helix	171-190	20
α-helix	193-199	7
α-helix	200-204	5
α-helix	215-233	19
α-helix	249-251	3
α-helix	252-284	33
α-helix	288-308	21
α-helix	310-312	3
α-helix	319-325	7
α-helix	330-348	19
β-strand	353	1	1
β-strand	355	1	2
α-helix	357-378	22
α-helix	380-382	3
α-helix	386-394	9
α-helix	396-397	2
α-helix	398-402	5
α-helix	405-416	12
α-helix	419-421	3
α-helix	422-438	17
α-helix	444-455	12

Chain B: 26 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	33-70	38
α-helix	75-100	26
α-helix	102-104	3
α-helix	109-116	8
α-helix	124-140	17
β-strand	146	1	3
α-helix	148-165	18
α-helix	171-190	20
α-helix	193-199	7
α-helix	200-204	5
α-helix	215-233	19
α-helix	249-251	3
α-helix	253-284	32
α-helix	288-308	21
α-helix	310-312	3
α-helix	319-324	6
α-helix	330-348	19
β-strand	355	1	3
α-helix	357-378	22
α-helix	380-382	3
α-helix	386-394	9
α-helix	396-397	2
α-helix	398-402	5
α-helix	405-416	12
α-helix	419-421	3
α-helix	422-438	17
α-helix	444-454	11

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-12	3	5
β-strand	18-25	8	4
β-strand	34-39	6	5
β-strand	45-51	7	5
β-strand	58-60	3	5
β-strand	68-73	6	4
β-strand	78-83	6	4
β-strand	92-100	9	5
β-strand	107-111	5	5
β-strand	115-119	5	5
α-helix	123-124	2
β-strand	125	1	6
α-helix	126-127	2
β-strand	128-132	5	7
α-helix	133-135	3
β-strand	143-153	11	7
β-strand	154	1	6
β-strand	159-162	4	8
α-helix	163-165	3
β-strand	171-173	3	7
α-helix	174-176	3
β-strand	177-179	3	7
β-strand	182-192	11	7
β-strand	201-207	7	8
α-helix	208-210	3
β-strand	212-218	7	8

Chain D: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-6	3	9
β-strand	11-13	3	10
β-strand	15	1	11
β-strand	17	1	11
β-strand	19-25	7	9
β-strand	33-37	5	12
β-strand	44-48	5	12
β-strand	52-53	2	12
α-helix	54	1
β-strand	61-66	6	9
β-strand	69-74	6	9
α-helix	79-81	3
β-strand	84-89	6	12
β-strand	96-97	2	12
β-strand	103-105	3	10
β-strand	110	1	13
β-strand	113-117	5	14
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	14
β-strand	139	1	13
β-strand	144-149	6	15
β-strand	152-154	3	15
β-strand	158-160	3	14
α-helix	162-166	5
β-strand	172-181	10	14
α-helix	182-186	5
β-strand	190-196	7	15
β-strand	204-209	6	15

Chain E: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-12	3	17
β-strand	18-25	8	16
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	58-60	3	17
β-strand	68-73	6	16
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-101	10	17
β-strand	106-111	6	17
β-strand	115-119	5	17
β-strand	125	1	18
α-helix	126-127	2
β-strand	128-132	5	19
β-strand	143-153	11	19
β-strand	154	1	18
β-strand	159-162	4	20
α-helix	163-165	3
β-strand	171-173	3	19
α-helix	174-176	3
β-strand	177-179	3	19
β-strand	182-192	11	19
β-strand	201-207	7	20
α-helix	208-210	3
β-strand	212-218	7	20

Chain F: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-6	3	21
β-strand	10-13	4	22
β-strand	15	1	23
β-strand	17	1	23
β-strand	18-25	8	21
β-strand	33-37	5	22
β-strand	44-48	5	22
β-strand	52-53	2	22
α-helix	54	1
β-strand	61-66	6	21
β-strand	69-75	7	21
α-helix	79-81	3
β-strand	84-89	6	22
α-helix	95	1
β-strand	96-97	2	22
β-strand	101-105	5	22
β-strand	110	1	24
β-strand	113-117	5	25
α-helix	121-124	4
β-strand	128-138	11	25
β-strand	139	1	24
β-strand	144-149	6	26
β-strand	152-154	3	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	190-196	7	26
α-helix	203	1
β-strand	204-209	6	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H(+)/Cl(-) exchange transporter ClcA	A, B	protein	446	Escherichia coli	P37019 (AlphaFold model)
Fab, heavy chain	C, E	protein	222	Mus musculus
Fab, light chain	D, F	protein	211	Mus musculus	P01837 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4KK8_1 H(+)/Cl(-) exchange transporter ClcA (chains A, B)
MRRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNY
PLLLTVAFLCSAVLAMFGYFLVRKYAPEAGGSGIPEIEGALEDQRPVRWWRVLPVKFFGG
LGTLGGGMVLGRQGPTVQIGGNIGRMVLDIFRLKGDEARHTLLATGAAAGLAAAFNAPLA
GILFIIEEMRPQFRYTLISIKAVFIGVIMSTIMYRIFNHEVALIDVGKLSDAPLNTLWLY
LILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVAPATSGG
GFNLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPMLALGTVLGTAFGMVA
VELFPQYHLEAGTFAIAGMGALLAASIRAPLTGIILVLEMTDNYQLILPMIITGLGATLL
AQFTGGKPLYSAILARTLAKQEAEQK

Sequence of entity 2 (C, E), FASTA

>4KK8_2 Fab, heavy chain (chains C, E)
EVRLLESGGGLVQPGGSLKLSCAASGFDYSRYWMSWVRQAPGKGLKWIGEINPVSSTINY
TPSLKDKFIISRDNAKDTLYLQISKVRSEDTALYYCARLYYGYGYWYFDVWGAGTTVTVS
SAKTTPPSVYPLAPGSAAAAASMVTLGCLVKGYFPEPVTVTWNSGSLAAGVHTFPAVLQA
ALYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRA

Sequence of entity 3 (D, F), FASTA

>4KK8_3 Fab, light chain (chains D, F)
DIVLTQSPAIMSAAPGDKVTMTCSASSSVSYIHWYQQKSGTSPKRWIYDTSKLTSGVPVR
FSGSGSGTSYSLTINTMEAEDAATYYCQQWSSHPQTFGGGTKLEILRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRA

Ligands and cofactors

ID	Name	Formula	Copies
F	Fluoride ion	F	2

Primary citation

Fluoride-dependent interruption of the transport cycle of a CLC Cl(-)/H(+) antiporter. Lim, H.H., Stockbridge, R.B., Miller, C. Nat Chem Biol (2013) 9:721-725. DOI 10.1038/nchembio.1336 · 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
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
8GAH 2.9 Å, CLC-ec1 L25C/A450C/C85A at pH 4.5 100mM Cl Twist

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