8CAF: N8C_Fab3b

N8C_Fab3b in complex with NEDD8-CUL1(WHB). Determined by X-ray diffraction at 2.66 Å resolution. Released 13 Sept 2023.

Method: X-ray diffraction
Resolution: 2.66 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,808
Mol. weight: 128.53 kDa
Released: 13 Sept 2023

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

Secondary structure: helices and β-sheets

8CAF contains 45 α-helices and 108 β-strands across 8 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
α-helix	43-44	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-91	8	2
β-strand	96-98	3	2
β-strand	102-107	6	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	33-39	7	7
β-strand	45-52	8	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-99	8	7
β-strand	112-113	2	7
β-strand	117-121	5	7
α-helix	125-126	2
β-strand	127	1	8
β-strand	130-134	5	9
β-strand	146-155	10	9
β-strand	156	1	8
β-strand	161-164	4	10
β-strand	169	1	10
β-strand	173-175	3	9
α-helix	176-178	3
β-strand	179-180	2	9
β-strand	186-194	9	9
β-strand	205-210	6	10
α-helix	211-213	3
β-strand	215-220	6	10

Chain C: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-91	7	12
β-strand	96-98	3	12
β-strand	102-106	5	12
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-154	2	15
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-188	6
β-strand	191-197	7	15
β-strand	205-210	6	15

Chain D: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	46-52	7	17
β-strand	58-60	3	17
α-helix	62-64	3
β-strand	68-73	6	16
β-strand	78-83	6	16
α-helix	88-90	3
β-strand	92-99	8	17
β-strand	112-113	2	17
β-strand	117-121	5	17
β-strand	127	1	18
α-helix	128-129	2
β-strand	130-134	5	19
β-strand	146-155	10	19
β-strand	156	1	18
β-strand	161-164	4	20
α-helix	165-167	3
β-strand	169	1	20
β-strand	173-175	3	19
α-helix	176-178	3
β-strand	179-180	2	19
β-strand	186-194	9	19
α-helix	196-198	3
β-strand	199	1	21
β-strand	202	1	21
β-strand	205-210	6	20
α-helix	211-213	3
β-strand	215-220	6	20

Chain E: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	699-722	24
β-strand	724-726	3	22
α-helix	727-738	12
α-helix	746-758	13
β-strand	762-764	3	22
α-helix	765	1
β-strand	771-774	4	22

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	23
β-strand	12-16	5	23
β-strand	22	1	24
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	23
β-strand	48-49	2	23
α-helix	50-51	2
β-strand	55	1	24
α-helix	57-59	3
β-strand	66-71	6	23

Chain G: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	25
β-strand	12-16	5	25
β-strand	22	1	26
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	25
β-strand	48-49	2	25
α-helix	50-51	2
β-strand	55	1	26
α-helix	57-59	3
β-strand	66-71	6	25

Chain H: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	703-722	20
β-strand	724-726	3	27
α-helix	727-738	12
α-helix	746-758	13
β-strand	762-764	3	27
β-strand	771-774	4	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab Light Chain	A, C	protein	211	Homo sapiens
Fab Heavy Chain	B, D	protein	223	Homo sapiens
Cullin-1	E, H	protein	79	Homo sapiens	Q13616 (AlphaFold model)
NEDD8	F, G	protein	76	Homo sapiens	Q15843 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8CAF_1 Fab Light Chain (chains A, C)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQSSYSLITFGQGTKVEIKRTVAAPSVFIFPP
SDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 2 (B, D), FASTA

>8CAF_2 Fab Heavy Chain (chains B, D)
EVQLVESGGGLVQPGGSLRLSCAASGFNFSSSSIHWVRQAPGKGLEWVASISSSYGYTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARDPFGWAAHGVGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 3 (E, H), FASTA

>8CAF_3 Cullin-1 (chains E, H)
TTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILI
EKEYLERVDGEKDTYSYLA

Sequence of entity 4 (F, G), FASTA

>8CAF_4 NEDD8 (chains F, G)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG

Primary citation

Activity-based profiling of cullin-RING E3 networks by conformation-specific probes. Henneberg, L.T., Singh, J., Duda, D.M. et al. Nat Chem Biol (2023) 19:1513-1523. DOI 10.1038/s41589-023-01392-5 · PubMed

Other PDB entries of the same protein (UniProt Q13616 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
5V89 1.55 Å, Structure of DCN4 PONY domain bound to CUL1 WHB
3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
7Z8R 2.7 Å, CAND1-CUL1-RBX1
7Z8V 2.7 Å, CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
8OR3 2.9 Å, CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
9QO4 2.95 Å, Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
1LDJ 3.0 Å, Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
4F52 3.0 Å, Structure of a Glomulin-RBX1-CUL1 complex
7Z8T 3.0 Å, CAND1-SCF-SKP2 CAND1 engaged SCF rocked
9XZL 3.0 Å, Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex…
9EFV 3.03 Å, Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3

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