2ZBF: PDB entry 2ZBF

Calcium pump crystal structure with bound BeF3 and TG in the absence of calcium. Determined by X-ray diffraction at 2.4 Å resolution. Released 11 Dec 2007.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Oryctolagus cuniculus
Chains: 1
Atoms: 8,036
Mol. weight: 110.37 kDa
Ligands: TG1, BEF, MG
Released: 11 Dec 2007

Explore 2ZBF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZBF contains 60 α-helices and 35 β-strands across 1 chain. 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: 60 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	9-16	8
β-strand	24	1	1
α-helix	26-36	11
α-helix	49-56	8
α-helix	60-77	18
α-helix	89-110	22
α-helix	119-121	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
α-helix	157	1
β-strand	158	1	3
α-helix	159	1
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	231-241	11
α-helix	248-272	25
α-helix	276-279	4
α-helix	295-306	12
α-helix	311-327	17
β-strand	331-333	3	4
α-helix	338-341	4
α-helix	342-344	3
β-strand	347-350	4	4
α-helix	352-356	5
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	470-476	7
β-strand	479-485	7	6
β-strand	493-500	8	6
α-helix	503-505	3
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
α-helix	559	1
β-strand	560-567	8	6
α-helix	570-572	3
α-helix	573-575	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	629-639	11
β-strand	652-654	3	4
α-helix	655-659	5
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	742-781	40
α-helix	783-785	3
α-helix	789-794	6
α-helix	795-799	5
α-helix	801-807	7
α-helix	810-813	4
α-helix	820-823	4
α-helix	831-857	27
α-helix	873-875	3
α-helix	890-892	3
α-helix	894-914	21
α-helix	927-929	3
α-helix	931-947	17
α-helix	952-956	5
α-helix	964-974	11
α-helix	976-989	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A	protein	995	Oryctolagus cuniculus	P04191 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2ZBF_1 Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (chains A)
XMEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFED
LLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEAL
KEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSI
LTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQM
AATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIA
VALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTN
QMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICAL
CNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLM
KKEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTG
PVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGM
LDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFD
DLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIA
MGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTA
ALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMA
IGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTM
ALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKL
KALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG

Ligands and cofactors

ID	Name	Formula	Copies
TG1	Octanoic acid [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z),…	C34 H50 O12	1
BEF	Beryllium trifluoride ion	Be F3	1
MG	Magnesium ion	Mg	1

Primary citation

How processing of aspartylphosphate is coupled to lumenal gating of the ion pathway in the calcium pump. Toyoshima, C., Norimatsu, Y., Iwasawa, S. et al. Proc Natl Acad Sci U S A (2007) 104:19831-19836. DOI 10.1073/pnas.0709978104 · 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
1WPG 2.3 Å, Crystal structure of the SR CA2+-ATPase with MGF4

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