8U84: BTB/POZ domain-containing protein KCTD5

Name: PDB 8U84: KCTD5/Cullin3/Gbeta1gamma2 Complex: State D From Composite RELION Multi-body Refinement Map
Published: 2023-10-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

KCTD5/Cullin3/Gbeta1gamma2 Complex: State D From Composite RELION Multi-body Refinement Map. Determined by electron microscopy at 3.88 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 3.88 Å
Organism: Homo sapiens
Chains: 20
Atoms: 37,885
Mol. weight: 579.61 kDa
Released: 11 Oct 2023

Explore 8U84 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U84 contains 199 α-helices and 193 β-strands across 20 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 B1: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-52	6	15
β-strand	58-63	6	16
β-strand	70-74	5	16
β-strand	78-81	4	16
β-strand	91-94	4	16
β-strand	100-105	6	17
β-strand	111-116	6	17
β-strand	121-125	5	17
β-strand	134-139	6	17
β-strand	146-151	6	18
β-strand	156-161	6	18
β-strand	168-170	3	18
β-strand	175-178	4	18
α-helix	186	1
β-strand	187	1	19
β-strand	191-192	2	20
β-strand	198-201	4	20
β-strand	203	1	19
β-strand	207-212	6	20
β-strand	218-223	6	20
β-strand	229-234	6	21
β-strand	240-245	6	21
β-strand	249-254	6	21
β-strand	260-265	6	21
α-helix	272	1
β-strand	273-278	6	22
β-strand	284-289	6	22
β-strand	294-298	5	22
β-strand	303-308	6	22
β-strand	315-320	6	15
β-strand	327-331	5	15
β-strand	335-339	5	15

Chain B2: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
β-strand	47-52	6	23
β-strand	58-63	6	24
β-strand	69-74	6	24
β-strand	78-83	6	24
β-strand	88-94	7	24
β-strand	100-105	6	25
α-helix	106	1
β-strand	111-116	6	25
β-strand	121-125	5	25
β-strand	134-139	6	25
β-strand	146-153	8	26
β-strand	156-161	6	26
β-strand	168-170	3	26
β-strand	176	1	26
β-strand	192	1	27
β-strand	198-202	5	27
β-strand	208-212	5	27
β-strand	217-222	6	27
β-strand	229-234	6	28
β-strand	240-245	6	28
β-strand	250-254	5	28
β-strand	259-264	6	28
β-strand	273-278	6	29
β-strand	284-289	6	29
β-strand	295-298	4	29
β-strand	303-307	5	29
β-strand	315-320	6	23
β-strand	327-331	5	23
β-strand	335-339	5	23

Chain B3: 3 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-52	6	30
β-strand	58-62	5	31
β-strand	69-74	6	31
β-strand	78-83	6	31
β-strand	88-94	7	31
β-strand	100-105	6	32
β-strand	111-116	6	32
β-strand	120-125	6	32
β-strand	134-140	7	32
β-strand	149-151	3	33
β-strand	156-159	4	33
β-strand	165	1	34
β-strand	168-170	3	33
β-strand	176	1	33
β-strand	181	1	34
β-strand	187	1	35
β-strand	192	1	36
β-strand	198-202	5	36
β-strand	203	1	35
β-strand	208-212	5	36
β-strand	220-222	3	36
β-strand	229-234	6	37
β-strand	240-245	6	37
β-strand	250-254	5	37
β-strand	260-264	5	37
β-strand	273-278	6	38
β-strand	284-289	6	38
β-strand	294-298	5	38
β-strand	304-308	5	38
β-strand	315-320	6	30
β-strand	327-331	5	30
β-strand	335-339	5	30

Chain B4: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-50	4	39
α-helix	57	1
β-strand	58-62	5	40
β-strand	71-74	4	40
β-strand	78-83	6	40
β-strand	88-94	7	40
α-helix	95	1
β-strand	102-105	4	41
β-strand	111-115	5	41
β-strand	120-125	6	41
β-strand	134-140	7	41
β-strand	146-151	6	42
β-strand	156-161	6	42
β-strand	168-170	3	42
β-strand	176-178	3	42
β-strand	187	1	43
β-strand	191-192	2	44
β-strand	198-202	5	44
β-strand	203	1	43
β-strand	208-212	5	44
β-strand	220-222	3	44
β-strand	229-234	6	45
β-strand	240-245	6	45
β-strand	249-254	6	45
β-strand	259-265	7	45
β-strand	273-278	6	46
β-strand	284-289	6	46
β-strand	294-298	5	46
β-strand	304-308	5	46
β-strand	315-320	6	39
β-strand	327-331	5	39
β-strand	336-339	4	39

Chain B5: 2 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
β-strand	47-51	5	47
β-strand	58-63	6	48
β-strand	69-74	6	48
β-strand	78-83	6	48
β-strand	88-94	7	48
β-strand	100-105	6	49
β-strand	111-116	6	49
β-strand	121-125	5	49
β-strand	134-139	6	49
β-strand	148-151	4	50
β-strand	156-160	5	50
β-strand	161	1	51
β-strand	165	1	51
β-strand	168-170	3	50
β-strand	175-178	4	50
β-strand	187-192	6	52
β-strand	198-203	6	52
β-strand	208-212	5	52
β-strand	218-222	5	52
β-strand	229-234	6	53
β-strand	240-245	6	53
β-strand	250-254	5	53
β-strand	259-264	6	53
β-strand	266	1	54
β-strand	269	1	54
β-strand	273-278	6	55
β-strand	284-289	6	55
β-strand	294-298	5	55
β-strand	303-308	6	55
β-strand	315-320	6	47
β-strand	327-331	5	47
β-strand	336-339	4	47

Chain C1: 27 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	28-45	18
α-helix	54-64	11
α-helix	65-69	5
α-helix	70-84	15
α-helix	85-90	6
α-helix	91-94	4
α-helix	101-122	22
α-helix	124-133	10
α-helix	139-147	9
α-helix	148-152	5
α-helix	155-174	20
α-helix	180-193	14
α-helix	199-201	3
α-helix	202-206	5
α-helix	207-227	21
α-helix	230-251	22
α-helix	254-256	3
α-helix	257-264	8
α-helix	265-269	5
α-helix	273-277	5
β-strand	278-279	2	13
β-strand	282-283	2	13
α-helix	284-288	5
α-helix	293-303	11
α-helix	309-329	21
α-helix	338-341	4
α-helix	344-355	12
α-helix	356-360	5
α-helix	364-378	15

Chain C2: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	27-45	19
α-helix	54-64	11
α-helix	65-69	5
α-helix	70-84	15
α-helix	85-89	5
α-helix	90-95	6
α-helix	101-122	22
α-helix	130-133	4
α-helix	139-147	9
α-helix	148-152	5
α-helix	155-173	19
α-helix	180-193	14
α-helix	199-201	3
α-helix	202-206	5
α-helix	207-227	21
α-helix	230-251	22
α-helix	254-256	3
α-helix	257-264	8
α-helix	265-269	5
β-strand	278-279	2	14
β-strand	282-283	2	14
α-helix	284-290	7
α-helix	293-303	11
α-helix	311-329	19
α-helix	344-358	15
α-helix	364-379	16

Chain C3: 27 helices, 0 β-strands

Element	Residues	Length
α-helix	27-45	19
α-helix	54-64	11
α-helix	65-69	5
α-helix	70-84	15
α-helix	85-90	6
α-helix	91-95	5
α-helix	101-122	22
α-helix	124-134	11
α-helix	136-138	3
α-helix	139-147	9
α-helix	148-152	5
α-helix	155-174	20
α-helix	180-193	14
α-helix	199-200	2
α-helix	201-206	6
α-helix	207-227	21
α-helix	230-251	22
α-helix	254-256	3
α-helix	257-265	9
α-helix	266-270	5
α-helix	275-277	3
α-helix	284-289	6
α-helix	293-305	13
α-helix	309-329	21
α-helix	344-355	12
α-helix	356-360	5
α-helix	364-378	15

11 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BTB/POZ domain-containing protein KCTD5	K1, K2, K3, K4, K5	protein	234	Homo sapiens	Q9NXV2 (AlphaFold model)
Cullin-3	C1, C2, C3, C4, C5	protein	381	Homo sapiens	Q13618 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B1, B2, B3, B4, B5	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G1, G2, G3, G4, G5	protein	71	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (K1, K2, K3, K4, K5), FASTA

>8U84_1 BTB/POZ domain-containing protein KCTD5 (chains K1, K2, K3, K4, K5)
MAENHCELLSPARGGIGAGLGGGLCRRCSAGLGALAQRPGSVSKWVRLNVGGTYFLTTRQ
TLCRDPKSFLYRLCQADPDLDSDKDETGAYLIDRDPTYFGPVLNYLRHGKLVINKDLAEE
GVLEEAEFYNITSLIKLVKDKIRERDSKTSQVPVKHVYRVLQCQEEELTQMVSTMSDGWK
FEQLVSIGSSYNYGNEDQAEFLCVVSKELHNTPYGTASEPSEKAKILQERGSRM

Sequence of entity 2 (C1, C2, C3, C4, C5), FASTA

>8U84_2 Cullin-3 (chains C1, C2, C3, C4, C5)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLN

Sequence of entity 3 (B1, B2, B3, B4, B5), FASTA

>8U84_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B1, B2, B3, B4, B5)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G1, G2, G3, G4, G5), FASTA

>8U84_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G1, G2, G3, G4, G5)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Primary citation

Structure and dynamics of a pentameric KCTD5/CUL3/G beta gamma E3 ubiquitin ligase complex. Nguyen, D.M., Rath, D.H., Devost, D. et al. Proc Natl Acad Sci U S A (2024) 121:e2315018121-e2315018121. DOI 10.1073/pnas.2315018121 · PubMed

Other PDB entries of the same protein (UniProt Q9NXV2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3DRZ 1.9 Å, X-ray crystal structure of the N-terminal BTB domain of human KCTD5 protein
8U7Z 2.97 Å, KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(CTD)/Gbeta1gamma2
3DRX 3.11 Å, X-ray crystal structure of human KCTD5 protein crystallized in high-salt buffer
3DRY 3.3 Å, X-ray crystal structure of human KCTD5 protein crystallized in low-salt buffer
8U80 3.6 Å, KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)/Cullin3(NTD)
8U81 3.82 Å, KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement…
8U82 3.84 Å, KCTD5/Cullin3/Gbeta1gamma2 Complex: State B From Composite RELION Multi-body Refinement…
8U83 3.98 Å, KCTD5/Cullin3/Gbeta1gamma2 Complex: State C From Composite RELION Multi-body Refinement…

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