6D1U: Human CLR:RAMP1 extracellular domain heterodimer

Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer in complex with adrenomedullin 2/intermedin. Determined by X-ray diffraction at 2.05 Å resolution. Released 5 Sept 2018.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Escherichia coli O157:H7, Homo sapiens
Chains: 6
Atoms: 14,158
Mol. weight: 205.81 kDa
Released: 5 Sept 2018

Explore 6D1U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D1U contains 105 α-helices and 106 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: 35 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	1
α-helix	19-33	15
β-strand	37-40	4	1
α-helix	45-53	9
β-strand	61-65	5	1
α-helix	66-68	3
α-helix	69-74	6
β-strand	78	1	2
α-helix	79-81	3
α-helix	85-88	4
β-strand	91	1	3
α-helix	93-98	6
β-strand	100-101	2	4
β-strand	104-105	2	4
β-strand	108-113	6	1
β-strand	116-120	5	5
β-strand	130	1	6
α-helix	134-142	9
β-strand	147-149	3	5
α-helix	156-158	3
α-helix	160-165	6
β-strand	169-174	6	7
β-strand	177-184	8	7
α-helix	188-202	15
α-helix	212-220	9
β-strand	224-229	6	5
α-helix	231-233	3
α-helix	234-240	7
β-strand	244-247	4	5
α-helix	248-250	3
β-strand	251	1	6
β-strand	252	1	8
β-strand	255	1	8
α-helix	259	1
β-strand	260-261	2	9
β-strand	262-268	7	1
β-strand	269	1	2
α-helix	275-281	7
α-helix	282-286	5
α-helix	289-298	10
β-strand	303-304	2	1
β-strand	306	1	3
α-helix	307-313	7
α-helix	317-328	12
β-strand	330-331	2	9
α-helix	332-333	2
α-helix	338-353	16
α-helix	359-371	13
α-helix	1026-1028	3
α-helix	1030-1035	6
α-helix	1036-1041	6
α-helix	1042-1051	10
α-helix	1053-1055	3
α-helix	1059-1079	21
α-helix	1087-1100	14
α-helix	2036-2054	19
α-helix	2056-2058	3
β-strand	2064-2065	2	10
β-strand	2068-2069	2	11
β-strand	2074-2075	2	11
β-strand	2078-2079	2	10
β-strand	2082-2087	6	12
α-helix	2088-2089	2
β-strand	2100-2105	6	12
β-strand	2111	1	12
β-strand	2113	1	13
β-strand	2120	1	13
β-strand	2123	1	12
α-helix	2125-2128	4

Chain B: 35 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	14
α-helix	19-33	15
β-strand	37-40	4	14
α-helix	45-53	9
β-strand	61-65	5	14
α-helix	66-68	3
α-helix	69-74	6
β-strand	78	1	15
α-helix	79-81	3
α-helix	85-88	4
β-strand	91	1	16
α-helix	93-98	6
β-strand	100-101	2	17
β-strand	104-105	2	17
β-strand	108-113	6	14
β-strand	116-120	5	18
β-strand	130	1	19
α-helix	134-142	9
β-strand	147-149	3	18
α-helix	156-158	3
α-helix	160-165	6
β-strand	169-174	6	20
β-strand	177-184	8	20
α-helix	188-202	15
α-helix	212-220	9
β-strand	224-229	6	18
α-helix	231-233	3
α-helix	234-240	7
β-strand	244-247	4	18
α-helix	248-250	3
β-strand	251	1	19
β-strand	252	1	21
β-strand	255	1	21
α-helix	259	1
β-strand	260-261	2	22
β-strand	262-268	7	14
β-strand	269	1	15
α-helix	275-281	7
α-helix	282-286	5
α-helix	289-298	10
β-strand	303-304	2	14
β-strand	306	1	16
α-helix	307-313	7
α-helix	317-328	12
β-strand	330-331	2	22
α-helix	332-333	2
α-helix	338-354	17
α-helix	359-371	13
α-helix	1026-1028	3
α-helix	1030-1035	6
α-helix	1036-1041	6
α-helix	1042-1051	10
α-helix	1053-1055	3
α-helix	1059-1079	21
α-helix	1087-1100	14
α-helix	2037-2054	18
α-helix	2056-2057	2
β-strand	2064-2065	2	23
β-strand	2068-2069	2	24
β-strand	2074-2075	2	24
β-strand	2078-2079	2	23
β-strand	2082-2087	6	25
α-helix	2088-2089	2
β-strand	2092	1	26
β-strand	2100-2105	6	25
β-strand	2111	1	25
β-strand	2113	1	27
β-strand	2120	1	27
β-strand	2123	1	25
α-helix	2125-2128	4

Chain C: 35 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	9-12	4	28
α-helix	19-33	15
β-strand	37-40	4	28
α-helix	45-53	9
β-strand	61-65	5	28
α-helix	66-68	3
α-helix	69-74	6
β-strand	78	1	29
α-helix	79-81	3
α-helix	85-88	4
β-strand	91	1	30
α-helix	93-98	6
β-strand	100-101	2	31
β-strand	104-105	2	31
β-strand	108-113	6	28
β-strand	116-120	5	32
β-strand	130	1	33
α-helix	134-142	9
β-strand	147-149	3	32
α-helix	156-158	3
α-helix	160-165	6
β-strand	169-174	6	34
β-strand	177-184	8	34
α-helix	188-202	15
α-helix	212-220	9
β-strand	224-229	6	32
α-helix	231-233	3
α-helix	234-240	7
β-strand	244-247	4	32
α-helix	248-250	3
β-strand	251	1	33
β-strand	252	1	35
β-strand	255	1	35
α-helix	259	1
β-strand	260-261	2	36
β-strand	262-268	7	28
β-strand	269	1	29
α-helix	275-281	7
α-helix	282-286	5
α-helix	289-298	10
β-strand	303-304	2	28
β-strand	306	1	30
α-helix	307-313	7
α-helix	317-328	12
β-strand	330-331	2	36
α-helix	332-333	2
α-helix	338-354	17
α-helix	359-370	12
α-helix	1031-1035	5
α-helix	1036-1041	6
α-helix	1042-1051	10
α-helix	1053-1055	3
α-helix	1059-1079	21
α-helix	1087-1100	14
α-helix	2036-2054	19
β-strand	2064-2065	2	37
β-strand	2068-2069	2	38
β-strand	2074-2075	2	38
β-strand	2078-2079	2	37
β-strand	2082-2087	6	39
α-helix	2088-2089	2
β-strand	2095	1	40
β-strand	2100-2105	6	39
β-strand	2111	1	39
β-strand	2113	1	41
β-strand	2120	1	41
β-strand	2123	1	39
α-helix	2125-2127	3
β-strand	2128	1	40
α-helix	2129-2147	19

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	34	1	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related…	A, B, C	protein	593	Escherichia coli O157:H7, Homo sapiens	O60894 (AlphaFold model), P0AEX9 (AlphaFold model), Q16602 (AlphaFold model)
ADM2	D, E, F	protein	20	Homo sapiens	Q7Z4H4 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6D1U_1 Maltose-binding periplasmic protein,Receptor activity-modifying protein 1,Calcitonin gene-related peptide type 1 receptor (chains A, B, C)
MAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPD
IIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYN
KDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDI
KDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTS
KVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKP
LGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVD
EALKDAQTNAAAEFTTACQEANYGALLRELCLTQFQVDMEAVGETLWCDWGRTIRSYREL
ADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPISGRAVGSAGSAGSAEDSIQLGVT
RNKIMTAQYECYQKIMQDPIQQAEGVYCNRTWDGWLCWNDVAAGTESMQLCPDYFQDFDP
SEKVTKICDQDGNWFRHPASNRTWTNYTQCNVNTHEKVKTALNLFYLHHHHHH

Sequence of entity 2 (D, E, F), FASTA

>6D1U_2 ADM2 (chains D, E, F)
GPAGRQDSAPVDPSSPHSYX

Primary citation

Structure-function analyses reveal a triple beta-turn receptor-bound conformation of adrenomedullin 2/intermedin and enable peptide antagonist design. Roehrkasse, A.M., Booe, J.M., Lee, S.M. et al. J Biol Chem (2018) 293:15840-15854. DOI 10.1074/jbc.RA118.005062 · PubMed

Other PDB entries of the same protein (UniProt O60894 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ZHO 1.6 Å, Crystal structure of a CGRP receptor ectodomain heterodimer with bound high affinity…
8AX7 1.65 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
7P0F 1.85 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
8AX6 1.9 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
3N7S 2.1 Å, Crystal structure of the ectodomain complex of the CGRP receptor, a Class-B GPCR,…
7TYF 2.2 Å, Human Amylin1 Receptor in complex with Gs and rat amylin peptide
9BP3 2.2 Å, Human Amylin1 Receptor in complex with Gs and cagrilintide
7P0I 2.3 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
2YX8 2.4 Å, Crystal structure of the extracellular domain of human RAMP1
9AUC 2.4 Å, Human Amylin1 Receptor in Complex with Gs and human Calcitonin Gene-Related Peptide
4RWG 2.44 Å, Crystal structure of the CLR:RAMP1 extracellular domain heterodimer with bound high…
6UMG 2.7 Å, Crystal structure of erenumab Fab bound to the extracellular domain of CGRP receptor

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