8U83: PDB entry 8U83

Name: PDB 8U83: KCTD5/Cullin3/Gbeta1gamma2 Complex: State C 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 C From Composite RELION Multi-body Refinement Map. Determined by electron microscopy at 3.98 Å resolution. Released 11 Oct 2023.

Method: Electron microscopy
Resolution: 3.98 Å
Organism: Homo sapiens
Chains: 20
Atoms: 37,885
Mol. weight: 579.61 kDa
Released: 11 Oct 2023

Explore 8U83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U83 contains 209 α-helices and 196 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: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
β-strand	47-50	4	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	148-150	3	4
β-strand	156-160	5	4
β-strand	168-170	3	4
β-strand	176	1	4
β-strand	187	1	5
β-strand	191-192	2	6
β-strand	198-201	4	6
β-strand	203	1	5
β-strand	207-212	6	6
β-strand	220-223	4	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain B2: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
β-strand	50-52	3	9
β-strand	58-63	6	10
β-strand	69-74	6	10
β-strand	78-83	6	10
β-strand	88-94	7	10
β-strand	100-105	6	11
β-strand	111-116	6	11
β-strand	120-125	6	11
β-strand	134-140	7	11
β-strand	146-150	5	12
β-strand	156-161	6	12
β-strand	165	1	12
β-strand	168-170	3	12
β-strand	175-178	4	12
β-strand	187	1	13
β-strand	191-192	2	14
β-strand	199-201	3	14
β-strand	203	1	13
β-strand	207-211	5	14
β-strand	218-223	6	14
β-strand	229-234	6	15
β-strand	240-245	6	15
β-strand	249-254	6	15
β-strand	259-265	7	15
α-helix	272	1
β-strand	273-278	6	16
β-strand	284-289	6	16
β-strand	295-298	4	16
β-strand	304-307	4	16
β-strand	315-320	6	9
β-strand	327-331	5	9
β-strand	335-339	5	9

Chain B3: 2 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
β-strand	47-50	4	17
β-strand	58	1	18
β-strand	62	1	19
β-strand	69-73	5	19
β-strand	74	1	18
β-strand	78-83	6	19
β-strand	88-94	7	19
β-strand	102-105	4	20
β-strand	111-115	5	20
β-strand	121-128	8	20
β-strand	132-139	8	20
β-strand	146-151	6	21
β-strand	156-161	6	21
β-strand	165	1	21
β-strand	168-170	3	21
β-strand	176-178	3	21
β-strand	187	1	22
β-strand	192	1	23
β-strand	198-201	4	23
β-strand	203	1	22
β-strand	208-212	5	23
β-strand	218-222	5	23
β-strand	229-234	6	24
β-strand	240-245	6	24
β-strand	250-254	5	24
β-strand	259-264	6	24
β-strand	273-277	5	25
β-strand	284-289	6	25
β-strand	294-298	5	25
β-strand	304-308	5	25
β-strand	317-320	4	17
β-strand	327-331	5	17
β-strand	335-339	5	17

Chain B4: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
β-strand	47-51	5	26
β-strand	58-63	6	27
β-strand	69-74	6	27
β-strand	78-83	6	27
β-strand	88-94	7	27
β-strand	102-105	4	28
β-strand	111-115	5	28
β-strand	120-125	6	28
β-strand	134-140	7	28
β-strand	146-150	5	29
β-strand	156-161	6	29
β-strand	165	1	29
β-strand	168-170	3	29
β-strand	176-178	3	29
β-strand	187-192	6	30
β-strand	198-203	6	30
β-strand	208-212	5	30
β-strand	218-222	5	30
β-strand	229-234	6	31
β-strand	240-245	6	31
β-strand	249-254	6	31
β-strand	259-265	7	31
β-strand	273-278	6	32
β-strand	284-289	6	32
β-strand	294-298	5	32
β-strand	303-308	6	32
β-strand	317-320	4	26
β-strand	327-330	4	26
β-strand	336-339	4	26

Chain B5: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-39	2
β-strand	43-44	2	33
β-strand	47-51	5	34
β-strand	58-60	3	35
β-strand	63	1	36
β-strand	70	1	36
β-strand	73-74	2	35
β-strand	78-83	6	35
β-strand	88-94	7	35
β-strand	100-105	6	37
β-strand	111-116	6	37
β-strand	121-125	5	37
β-strand	135-139	5	37
β-strand	148-151	4	38
β-strand	156-161	6	38
β-strand	165-170	6	38
β-strand	175-178	4	38
β-strand	187-189	3	39
β-strand	198-203	6	39
β-strand	208-212	5	39
β-strand	218-222	5	39
β-strand	229-234	6	40
β-strand	240-245	6	40
β-strand	249-254	6	40
β-strand	259-265	7	40
β-strand	273-278	6	33
β-strand	284-289	6	33
β-strand	294-298	5	33
β-strand	304-308	5	33
β-strand	315-320	6	34
β-strand	327-331	5	34
β-strand	336-339	4	34

Chain C1: 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	85-90	6
α-helix	91-94	4
α-helix	101-122	22
α-helix	124-128	5
α-helix	130-133	4
α-helix	139-149	11
α-helix	155-173	19
α-helix	180-192	13
α-helix	198-201	4
α-helix	202-206	5
α-helix	207-227	21
α-helix	230-246	17
α-helix	247-251	5
α-helix	257-264	8
α-helix	265-269	5
β-strand	279	1	41
β-strand	282	1	41
α-helix	284-290	7
α-helix	293-303	11
α-helix	309-329	21
α-helix	344-358	15
α-helix	364-378	15

Chain C2: 27 helices, 0 β-strands

Element	Residues	Length
α-helix	38-45	8
α-helix	54-57	4
α-helix	70-84	15
α-helix	85-90	6
α-helix	91-94	4
α-helix	101-122	22
α-helix	124-126	3
α-helix	127-131	5
α-helix	132-133	2
α-helix	139-147	9
α-helix	148-152	5
α-helix	155-174	20
α-helix	181-193	13
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	285-290	6
α-helix	293-303	11
α-helix	311-329	19
α-helix	338-341	4
α-helix	343-354	12
α-helix	355-359	5
α-helix	364-378	15

Chain C3: 30 helices, 0 β-strands

Element	Residues	Length
α-helix	30-45	16
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	124-125	2
α-helix	126-130	5
α-helix	131-133	3
α-helix	136-138	3
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	257-265	9
α-helix	266-270	5
α-helix	273-277	5
α-helix	284-289	6
α-helix	293-303	11
α-helix	309-329	21
α-helix	338	1
α-helix	339-343	5
α-helix	344-359	16
α-helix	364-379	16

12 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
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)
Cullin-3	C1, C2, C3, C4, C5	protein	381	Homo sapiens	Q13618 (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)
BTB/POZ domain-containing protein KCTD5	K1, K2, K3, K4, K5	protein	234	Homo sapiens	Q9NXV2 (AlphaFold model)

Sequence of entity 1 (B1, B2, B3, B4, B5), FASTA

>8U83_1 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 2 (C1, C2, C3, C4, C5), FASTA

>8U83_2 Cullin-3 (chains C1, C2, C3, C4, C5)
MSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRN
AYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDHQTAMVMIR
DILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARERKGEVVDR
GAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASVYIKKVEAR
INEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGKTEDLGCMY
KLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRFDRFLLESF
NNDRLFKQTIAGDFEYFLNLN

Sequence of entity 3 (G1, G2, G3, G4, G5), FASTA

>8U83_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G1, G2, G3, G4, G5)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Sequence of entity 4 (K1, K2, K3, K4, K5), FASTA

>8U83_4 BTB/POZ domain-containing protein KCTD5 (chains K1, K2, K3, K4, K5)
MAENHCELLSPARGGIGAGLGGGLCRRCSAGLGALAQRPGSVSKWVRLNVGGTYFLTTRQ
TLCRDPKSFLYRLCQADPDLDSDKDETGAYLIDRDPTYFGPVLNYLRHGKLVINKDLAEE
GVLEEAEFYNITSLIKLVKDKIRERDSKTSQVPVKHVYRVLQCQEEELTQMVSTMSDGWK
FEQLVSIGSSYNYGNEDQAEFLCVVSKELHNTPYGTASEPSEKAKILQERGSRM

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 P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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