1WPG: SR CA2+-ATPase with MGF4

Crystal structure of the SR CA2+-ATPase with MGF4. Determined by X-ray diffraction at 2.3 Å resolution. Released 5 Oct 2004.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Oryctolagus cuniculus
Chains: 4
Atoms: 31,698
Mol. weight: 443.41 kDa
Ligands: MG, MF4, ADP, TG1
Released: 5 Oct 2004

Explore 1WPG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1WPG contains 249 α-helices and 136 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: 61 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	9-16	8
β-strand	24	1	1
α-helix	26-35	10
α-helix	41-43	3
α-helix	49-56	8
α-helix	60-77	18
α-helix	89-110	22
α-helix	115-119	5
α-helix	120-122	3
β-strand	126-130	5	2
β-strand	131	1	1
β-strand	138-141	4	2
α-helix	142-144	3
β-strand	150-154	5	2
β-strand	158	1	3
β-strand	162-168	7	2
β-strand	174-176	3	3
α-helix	178-181	4
α-helix	186	1
β-strand	187-188	2	3
α-helix	189	1
α-helix	201-203	3
β-strand	207-208	2	2
β-strand	213-216	4	3
β-strand	218-225	8	2
α-helix	227-229	3
α-helix	231-239	9
α-helix	244-247	4
α-helix	248-274	27
α-helix	292-294	3
α-helix	295-306	12
α-helix	311-327	17
β-strand	331-333	3	4
α-helix	338-342	5
β-strand	347-350	4	4
β-strand	357	1	5
β-strand	362-373	12	6
β-strand	376-384	9	6
β-strand	395-397	3	6
β-strand	400-401	2	6
α-helix	404-406	3
α-helix	408-419	12
β-strand	424-428	5	7
β-strand	433-437	5	7
α-helix	440-452	13
α-helix	464-467	4
α-helix	470-478	9
β-strand	479-488	10	6
β-strand	493-500	8	6
α-helix	503-508	6
β-strand	511-516	6	6
α-helix	518-523	6
β-strand	525-530	6	6
β-strand	533-536	4	6
α-helix	539-552	14
β-strand	560-567	8	6
α-helix	570-572	3
α-helix	573-575	3
α-helix	581-583	3
α-helix	584-587	4
β-strand	591-600	10	6
α-helix	602	1
β-strand	603	1	5
α-helix	604	1
α-helix	607-616	10
β-strand	620-624	5	4
α-helix	629-638	10
β-strand	652-654	3	4
α-helix	655-660	6
α-helix	663-672	10
β-strand	675-677	3	4
α-helix	681-693	13
β-strand	698-702	5	4
α-helix	705-707	3
α-helix	708-713	6
β-strand	716-720	5	4
α-helix	725-729	5
β-strand	733-735	3	4
α-helix	741-780	40
α-helix	789-794	6
α-helix	795-799	5
α-helix	801-807	7
α-helix	810-812	3
α-helix	815-818	4
α-helix	820-823	4
α-helix	832-855	24
α-helix	869-872	4
α-helix	888-892	5
α-helix	894-913	20
α-helix	927-929	3
α-helix	931-949	19
α-helix	954-957	4
α-helix	964-974	11
α-helix	976-987	12
α-helix	988-992	5

Chains B and C: 64 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
α-helix	26-36	11
α-helix	41-43	3
α-helix	45-48	4
α-helix	49-54	6
α-helix	55-57	3
α-helix	60-74	15
α-helix	75-77	3
α-helix	89-109	21
α-helix	115-119	5
α-helix	120-122	3
β-strand	126-130	5	8
β-strand	138-141	4	8
α-helix	142-144	3
β-strand	150-154	5	8
α-helix	157	1
β-strand	158	1	9
α-helix	159	1
β-strand	162-168	7	8
β-strand	174-176	3	9
α-helix	178-181	4
α-helix	186	1
β-strand	187-188	2	9
α-helix	189	1
α-helix	201-203	3
β-strand	207-208	2	8
β-strand	213-216	4	9
β-strand	218-225	8	8
α-helix	227-229	3
α-helix	231-240	10
α-helix	244-247	4
α-helix	248-274	27
α-helix	277-279	3
α-helix	284-286	3
α-helix	288-306	19
α-helix	311-328	18
β-strand	331-333	3	10
α-helix	338-342	5
β-strand	347-350	4	10
β-strand	357	1	11
β-strand	362-373	12	12
β-strand	376-384	9	12
β-strand	395-397	3	12
β-strand	400-401	2	12
α-helix	404-406	3
α-helix	408-419	12
β-strand	424-428	5	13
β-strand	433-437	5	13
α-helix	440-452	13
α-helix	464-467	4
α-helix	470-478	9
β-strand	479-488	10	12
β-strand	493-500	8	12
α-helix	507	1
β-strand	511-516	6	12
α-helix	518-523	6
β-strand	525-530	6	12
β-strand	533-536	4	12
α-helix	539-552	14
β-strand	560-567	8	12
α-helix	570-572	3
α-helix	573-575	3
α-helix	581-583	3
α-helix	584-587	4
β-strand	591-600	10	12
α-helix	602	1
β-strand	603	1	11
α-helix	604	1
α-helix	607-616	10
β-strand	620-624	5	10
α-helix	629-638	10
β-strand	652-654	3	10
α-helix	655-660	6
α-helix	663-672	10
β-strand	675-677	3	10
α-helix	681-692	12
β-strand	698-702	5	10
α-helix	705-707	3
α-helix	708-713	6
β-strand	716-720	5	10
α-helix	725-729	5
β-strand	733-735	3	10
α-helix	741-780	40
α-helix	789-794	6
α-helix	795-799	5
α-helix	801-807	7
α-helix	810-813	4
α-helix	815-818	4
α-helix	820-823	4
α-helix	832-855	24
α-helix	869-872	4
α-helix	888-890	3
α-helix	894-913	20
α-helix	927-929	3
α-helix	931-949	19
α-helix	964-970	7
α-helix	976-991	16

Chain D: 60 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	9-16	8
β-strand	24	1	20
α-helix	26-35	10
α-helix	41-43	3
α-helix	49-56	8
α-helix	60-77	18
α-helix	89-110	22
α-helix	115-119	5
α-helix	120-122	3
β-strand	126-130	5	21
β-strand	131	1	20
β-strand	138-141	4	21
α-helix	142-144	3
β-strand	150-154	5	21
β-strand	158	1	22
β-strand	162-168	7	21
β-strand	174-176	3	22
α-helix	178-181	4
α-helix	186	1
β-strand	187-188	2	22
α-helix	189	1
α-helix	201-203	3
β-strand	207-208	2	21
β-strand	213-216	4	22
β-strand	218-225	8	21
α-helix	227-229	3
α-helix	231-239	9
α-helix	244-247	4
α-helix	248-274	27
α-helix	292-294	3
α-helix	295-306	12
α-helix	311-327	17
β-strand	331-333	3	23
α-helix	338-342	5
β-strand	347-350	4	23
β-strand	357	1	24
β-strand	362-373	12	25
β-strand	376-384	9	25
β-strand	395-397	3	25
β-strand	400-401	2	25
α-helix	404-406	3
α-helix	408-419	12
β-strand	424-428	5	26
β-strand	433-437	5	26
α-helix	440-452	13
α-helix	464-467	4
α-helix	470-478	9
β-strand	479-488	10	25
β-strand	493-500	8	25
α-helix	503-508	6
β-strand	511-516	6	25
α-helix	518-523	6
β-strand	525-530	6	25
β-strand	533-536	4	25
α-helix	539-552	14
β-strand	560-567	8	25
α-helix	570-572	3
α-helix	573-575	3
α-helix	581-583	3
α-helix	584-587	4
β-strand	591-600	10	25
α-helix	602	1
β-strand	603	1	24
α-helix	604	1
α-helix	607-616	10
β-strand	620-624	5	23
α-helix	629-638	10
β-strand	652-654	3	23
α-helix	655-660	6
α-helix	663-672	10
β-strand	675-677	3	23
α-helix	681-693	13
β-strand	698-702	5	23
α-helix	708-713	6
β-strand	716-720	5	23
α-helix	725-729	5
β-strand	733-735	3	23
α-helix	741-780	40
α-helix	789-794	6
α-helix	795-799	5
α-helix	801-807	7
α-helix	810-812	3
α-helix	815-818	4
α-helix	820-823	4
α-helix	832-855	24
α-helix	869-872	4
α-helix	888-892	5
α-helix	894-913	20
α-helix	927-929	3
α-helix	931-949	19
α-helix	954-957	4
α-helix	964-974	11
α-helix	976-987	12
α-helix	988-992	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A, B, C, D	protein	994	Oryctolagus cuniculus	P04191 (AlphaFold model)

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

>1WPG_1 Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (chains A, B, C, D)
MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDL
LVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALK
EYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSIL
TGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMA
ATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAV
ALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQ
MSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALC
NDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMK
KEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGP
VKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML
DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDD
LPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAM
GSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAA
LGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAI
GGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMA
LSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLK
ALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
MF4	TETRAFLUOROMAGNESATE(2-)	F4 Mg	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4
TG1	Octanoic acid [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z),…	C34 H50 O12	4

Water and common crystallization additives (NA) are not listed.

Primary citation

Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues. Toyoshima, C., Nomura, H., Tsuda, T. Nature (2004) 432:361-368. DOI 10.1038/nature02981 · PubMed

Other PDB entries of the same protein (UniProt P04191 (AlphaFold model), which also has an AlphaFold model), best resolution first:

27RD 2.0 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound IPP
27QZ 2.1 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound B1HQ
27RC 2.1 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound BMP
27QY 2.12 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound AHQ
3AR4 2.15 Å, Calcium pump crystal structure with bound ATP and TG in the absence of Ca2+
3AR7 2.15 Å, Calcium pump crystal structure with bound TNP-ATP and TG in the absence of Ca2+
27RE 2.2 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound MPQ
27RF 2.2 Å, Crystal structure of SR Ca2+-ATPase in E2(TG) with bound PHQ
3AR5 2.2 Å, Calcium pump crystal structure with bound TNP-AMP and TG
3AR6 2.2 Å, Calcium pump crystal structure with bound TNP-ADP and TG in the absence of calcium
3N5K 2.2 Å, Structure Of The (Sr)Ca2+-ATPase E2-AlF4- Form
3AR3 2.3 Å, Calcium pump crystal structure with bound ADP and TG

Browse structure collections

About this viewer

MolViewer shows 1WPG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.