7XUR: Human mini-SNAPc

The cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE. Determined by electron microscopy at 3.49 Å resolution. Released 7 Dec 2022.

Method: Electron microscopy
Resolution: 3.49 Å
Organisms: Homo sapiens, synthetic construct
Chains: 5
Atoms: 7,749
Mol. weight: 162.81 kDa
Ligands: ZN
Released: 7 Dec 2022

Explore 7XUR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XUR contains 43 α-helices and 25 β-strands across 3 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: 21 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-171	9
α-helix	177-179	3
α-helix	186-199	14
α-helix	241-246	6
α-helix	250-253	4
α-helix	264	1
α-helix	265-270	6
α-helix	279-287	9
α-helix	299-312	14
α-helix	317-323	7
α-helix	330-340	11
α-helix	351-363	13
β-strand	366	1	1
β-strand	369	1	1
α-helix	372-378	7
α-helix	384-390	7
α-helix	391-395	5
α-helix	406-419	14
α-helix	424-430	7
α-helix	436-445	10
α-helix	458-471	14
α-helix	477-482	6
α-helix	488-501	14

Chain B: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	2
β-strand	39	1	2
β-strand	42	1	3
α-helix	44-55	12
α-helix	56-58	3
α-helix	78-89	12
α-helix	94-103	10
α-helix	128-141	14
α-helix	151-160	10
β-strand	180-187	8	4
α-helix	188-190	3
α-helix	194-196	3
β-strand	201-207	7	4
β-strand	211	1	5
α-helix	213-216	4
α-helix	222-224	3
β-strand	251-254	4	4
β-strand	257-260	4	4
α-helix	272-277	6
β-strand	289-292	4	4
α-helix	293-295	3
β-strand	297	1	5
α-helix	298-300	3
β-strand	303	1	3
β-strand	308-313	6	4
β-strand	317-322	6	4
β-strand	324-328	5	4
β-strand	342-343	2	4
β-strand	353	1	6
β-strand	361	1	6
β-strand	364-367	4	7
β-strand	377-379	3	7
α-helix	381-387	7
β-strand	400-403	4	7
α-helix	407-410	4

Chain C: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
α-helix	26-35	10
α-helix	38-40	3
α-helix	48-66	19
α-helix	72-88	17
β-strand	97-99	3	8
α-helix	104-116	13
α-helix	120-131	12
β-strand	135-137	3	8
β-strand	138	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
snRNA-activating protein complex subunit 4	A	protein	522	Homo sapiens	Q5SXM2 (AlphaFold model)
snRNA-activating protein complex subunit 3	B	protein	411	Homo sapiens	Q92966 (AlphaFold model)
snRNA-activating protein complex subunit 1	C	protein	282	Homo sapiens	Q16533 (AlphaFold model)
DNA (35-mer)	X	DNA	35	synthetic construct
DNA (35-mer)	Y	DNA	35	synthetic construct

Sequence of entity 1 (A), FASTA

>7XUR_1 snRNA-activating protein complex subunit 4 (chains A)
DYKDDDDKSLEVLFQGPMDVDAEREKITQEIKELERILDPGSSGSHVEISESSLESDSEA
DSLPSEDLDPADPPISEEERWGEASNDEDDPKDKTLPEDPETCLQLNMVYQEVIQEKLAE
ANLLLAQNREQQEELMRDLAGSKGTKVKDGKSLPPSTYMGHFMKPYFKDKVTGVGPPANE
DTREKAAQGIKAFEELLVTKWKNWEKALLRKSVVSDRLQRLLQPKLLKLEYLHQKQSKVS
SELERQALEKQGREAEKEIQDINQLPEEALLGNRLDSHDWEKISNINFEGSRSAEEIRKF
WQNSEHPSINKQEWSREEEERLQAIAAAHGHLEWQKIAEELGTSRSAFQCLQKFQQHNKA
LKRKEWTEEEDRMLTQLVQEMRVGSHIPYRRIVYYMEGRDSMQLIYRWTKSLDPGLKKGY
WAPEEDAKLLQAVAKYGEQDWFKIREEVPGRSDAQCRDRYLRRLHFSLKKGRWNLKEEEQ
LIELIEKYGVGHWAKIASELPHRSGSQCLSKWKIMMGKKQGL

Sequence of entity 2 (B), FASTA

>7XUR_2 snRNA-activating protein complex subunit 3 (chains B)
MAEGSRGGPTCSGVGGRQDPVSGSGGCNFPEYELPELNTRAFHVGAFGELWRGRLRGAGD
LSLREPPASALPGSQAADSDREDAAVARDLDCSLEAAAELRAVCGLDKLKCLEDGEDPEV
IPENTDLVTLGVRKRFLEHREETITIDRACRQETFVYEMESHAIGKKPENSADMIEEGEL
ILSVNILYPVIFHKHKEHKPYQTMLVLGSQKLTQLRDSIRCVSDLQIGGEFSNTPDQAPE
HISKDLYKSAFFYFEGTFYNDKRYPECRDLSRTIIEWSESHDRGYGKFQTARMEDFTFND
LCIKLGFPYLYCHQGDCEHVIVITDIRLVHHDDCLDRTLYPLLIKKHWLWTRKCFVCKMY
TARWVTNNDSFAPEDPCFFCDVCFRMLHYDSEGNKLGEFLAYPYVDPGTFN

Sequence of entity 3 (C), FASTA

>7XUR_3 snRNA-activating protein complex subunit 1 (chains C)
HHHHHHSENLYFQGMGTPPGLQTDCEALLSRFQETDSVRFEDFTELWRNMKFGTIFCGRM
RNLEKNMFTKEALALAWRYFLPPYTFQIRVGALYLLYGLYNTQLCQPKQKIRVALKDWDE
VLKFQQDLVNAQHFDAAYIFRKLRLDRAFHFTAMPKLLSYRMKKKIHRAEVTEEFKDPSD
RVMKLITSDVLEEMLNVHDHYQNMKHVISVDKSKPDKALSLIKDDFFDNIKNIVLEHQQW
HKDRKNPSLKSKTNDGEEKMEGNSQETERCERAESLAKIKSK

Sequence of entity 4 (X), FASTA

>7XUR_4 DNA (35-MER) (chains X)
TCATATGCTTACCGTAACTTGAAAGTATTTCGATT

Sequence of entity 5 (Y), FASTA

>7XUR_5 DNA (35-MER) (chains Y)
AATCGAAATACTTTCAAGTTACGGTAAGCATATGA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter. Sun, J., Li, X., Hou, X. et al. Nat Commun (2022) 13:6871-6871. DOI 10.1038/s41467-022-34639-1 · PubMed

Other PDB entries of the same protein (UniProt Q5SXM2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZWD 3.0 Å, Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter…
7ZX8 3.0 Å, Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter…
9K3U 3.0 Å, Human RNA Polymerase III de novo transcribing complex 5 (TC5)
7ZWC 3.2 Å, Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter
9FSO 3.28 Å, Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1)
9LXN 3.3 Å, Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP)
9FSP 3.39 Å, RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2)
7ZX7 3.4 Å, Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter…
8IUH 3.4 Å, RNA polymerase III pre-initiation complex open complex 1
7ZXE 3.5 Å, Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter…
9K3V 3.5 Å, Human RNA Polymerase III de novo transcribing complex 4 (TC4)
9FSQ 3.51 Å, RNA Polymerase III Class III Melting Pre-Initiation Complex (MC)

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