7UL3: Inactive H2R

CryoEM Structure of Inactive H2R Bound to Famotidine, Nb6M, and NabFab. Determined by electron microscopy at 3.0 Å resolution. Released 29 Jun 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 5,484
Mol. weight: 108.47 kDa
Ligands: FO9
Released: 29 Jun 2022

Explore 7UL3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UL3 contains 27 α-helices and 49 β-strands across 4 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	17-45	29
α-helix	54-66	13
α-helix	67-71	5
α-helix	72-81	10
α-helix	88-103	16
α-helix	108-121	14
α-helix	126-129	4
α-helix	132-152	21
α-helix	182-186	5
α-helix	187-192	6
α-helix	193-211	19
α-helix	223-260	38
α-helix	267-291	25
α-helix	293-302	10

Chain C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
β-strand	13	1	2
β-strand	20-26	7	1
β-strand	32-41	10	3
β-strand	48-54	7	3
β-strand	59-61	3	3
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-102	10	3
α-helix	108	1
β-strand	109-113	5	3
β-strand	117-119	3	3
β-strand	120	1	2

Chain H: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	12	1	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	32-39	8	6
β-strand	45-50	6	6
β-strand	58-59	2	6
β-strand	67-71	5	4
β-strand	78-82	5	4
α-helix	84-86	3
β-strand	88-96	9	6
α-helix	99-100B	4
β-strand	103	1	6
β-strand	107-109	3	6
β-strand	111	1	5
β-strand	120-124	5	7
β-strand	138-143	6	7
β-strand	151-153	3	8
β-strand	164-165	2	7
α-helix	166-168	3
β-strand	178-182	5	7
β-strand	197-200	4	8
β-strand	205-206	2	8

Chain L: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	9
β-strand	22-24	3	10
α-helix	31-33	3
β-strand	34-38	5	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-65	4	10
β-strand	70-75	6	10
β-strand	85-90	6	9
β-strand	97-98	2	9
β-strand	102-105	4	9
α-helix	113	1
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	11
β-strand	145-150	6	12
β-strand	153-154	2	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-188	6
β-strand	191-197	7	12
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histamine H2 receptor	A	protein	400	Homo sapiens	P25021 (AlphaFold model), P41145 (AlphaFold model)
Nanobody 6M	C	protein	131	synthetic construct
NabFab HC	H	protein	239	synthetic construct
NabFab LC	L	protein	215	synthetic construct

Sequence of entity 1 (A), FASTA

>7UL3_1 Histamine H2 receptor (chains A)
DYKDDDDAMGQPGNGSAFLLAPNRSHAPDHDVENLYFQGMAPNGTASSFCLDSTACKITI
TVVLAVLILITVAGNVVVCLAVGLNRRLRNLTNCFIVSLAITDLLLGLLVLPFSAIYQLS
CKWSFGKVFCNIYTSLDVMLCTASILNLFMISLDRYCAVMDPLRYPVLVTPVRVAISLVL
IWVISITLSFLSIHLGWNSRNETSKGNHTTSKCKVQVNEVYGLVDGLVTFYLPLLIMCVC
YTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVICWFPYFTAFVYRGLRGDDAI
NEVLEAIVLWLGYANSALNPILYAALNRDFRTGYQQLFCCRLANRNSHKTSLRSNASQLS
RTQSREPRQQEEKPLKLQVWSGTEVTAPQGATDRLEVLFQ

Sequence of entity 2 (C), FASTA

>7UL3_2 Nanobody 6M (chains C)
QRQLVESGGGLVQPGGSLRLSCAASGTIFRLYDMGWFRQAPGKEREGVASITSGGSTKYA
DSVKGRFTISRDNAKNTVYLQMNSLEPEDTAVYYCNAEYRTGIWEELLDGWGKGTPVTVS
SHHHHHHEPEA

Sequence of entity 3 (H), FASTA

>7UL3_3 NabFab HC (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSYYSIHWVRQAPGKGLEWVAYISSSSSY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGYQYWQYHASWYWNGGLDY
WGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 4 (L), FASTA

>7UL3_4 NabFab LC (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
FO9	famotidine	C8 H17 N7 O2 S3	1

Primary citation

Structure determination of inactive-state GPCRs with a universal nanobody. Robertson, M.J., Papasergi-Scott, M.M., He, F. et al. Nat Struct Mol Biol (2022) 29:1188-1195. DOI 10.1038/s41594-022-00859-8 · PubMed

Other PDB entries of the same protein (UniProt P25021 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YN3 2.56 Å, Cryo-EM structure of histamine H2 receptor in complex with histamine and miniGs
8YUT 2.7 Å, Cryo-EM structure of the amthamine-bound H2R-Gs complex
9IXJ 2.92 Å, histamine-bound H2R in complex with Gs
8YN4 2.97 Å, Cryo-EM structure of histamine H2 receptor in complex with histamine and miniGq
8POK 3.4 Å, Cryo-EM structure of cell-free synthesized human histamine H2 receptor coupled to…

Browse structure collections

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