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- PDB-1wpg: Crystal structure of the SR CA2+-ATPase with MGF4 -

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Basic information

Entry
Database: PDB / ID: 1wpg
TitleCrystal structure of the SR CA2+-ATPase with MGF4
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / P-type Ca2+ transporter / P-type calcium transporter activity ...positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / haloacid dehalogenase-like hydrolase / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus ...Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / haloacid dehalogenase-like hydrolase / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / HAD superfamily/HAD-like / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROMAGNESATE(2-) / Chem-TG1 / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsToyoshima, C. / Nomura, H. / Tsuda, T.
Citation
Journal: Nature / Year: 2004
Title: Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
Authors: Toyoshima, C. / Nomura, H. / Tsuda, T.
#1: Journal: Nature / Year: 2000
Title: Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution
Authors: Toyoshima, C. / Nakasako, M. / Nomura, H. / Ogawa, H.
#2: Journal: Nature / Year: 2002
Title: Structural changes in the calcium pump accompanying the dissociation of calcium
Authors: Toyoshima, C. / Nomura, H.
#3: Journal: Nature / Year: 2004
Title: Crystal structure of the calcium pump with a bound ATP analogue
Authors: Toyoshima, C. / Mizutani, T.
History
DepositionSep 2, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
C: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
D: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,41028
Polymers438,4104
Non-polymers4,99924
Water12,430690
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.210, 275.394, 109.945
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.02111, 0.15929, 0.98701), (0.17329, -0.97287, 0.1533), (0.98464, 0.1678, -0.04815)76.19198, -5.31857, -86.25955
2given(0.02182, 0.15925, 0.987), (-0.17334, 0.97288, -0.15314), (-0.98462, -0.16774, 0.04883)25.01387, 16.88995, 141.2393
3given(1, 0.00019, 0.00031), (0.00019, -1, -8.0E-5), (0.00031, 8.0E-5, -1)-51.12693, 11.57827, 54.94005
4given(1, 0.00016, 0.00069), (0.00016, -1, -5.0E-5), (0.00069, 5.0E-5, -1)-51.1179, 11.55484, 54.92764
5given(0.02145, 0.17316, 0.98466), (-0.15937, 0.97289, -0.16761), (-0.98699, -0.15333, 0.04847)33.0959, 14.4372, 133.50566
6given(0.02216, -0.1732, -0.98464), (-0.15933, -0.9729, 0.16755), (-0.98698, 0.15317, -0.04915)90.31373, 8.33135, 83.98351

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / CA2+-ATPASE / SERCA1


Mass: 109602.578 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle (white) / References: UniProt: P04191, EC: 3.6.3.8

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Non-polymers , 6 types, 714 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MF4 / TETRAFLUOROMAGNESATE(2-) / MAGNESIUMTETRAFLUORIDE


Mass: 100.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: F4Mg
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical
ChemComp-TG1 / OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER / THAPSIGARGIN


Mass: 650.754 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H50O12
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE C-TERMINAL RESIDUES IN SWS ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, ...THE C-TERMINAL RESIDUES IN SWS ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, THERE IS ONLY ONE C-TERMINAL RESIDUE 994 G.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 63.17 %
Crystal growMethod: microdialysis / pH: 6.1 / Details: PEG400, pH 6.10, MICRODIALYSIS

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.8
SYNCHROTRONSPring-8 BL44XU20.9
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEMay 30, 2003
MAC Science DIP-20402IMAGE PLATEApr 13, 2002
RadiationMonochromator: ROTATED-INCLINED DOUBLE- CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
20.91
ReflectionResolution: 2.3→20 Å / Num. obs: 250560 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 5.07 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 25.14
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.432 / % possible all: 81.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3 CYTOPLASMIC DOMAINS OF CA2+-ATPASE IN 1FQU

1fqu


Resolution: 2.3→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 410979.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 12415 5 %RANDOM
Rwork0.223 ---
all0.23 ---
obs0.229 249271 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.47 Å2 / ksol: 0.328798 e/Å3
Displacement parametersBiso mean: 59.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.74 Å20 Å20 Å2
2--0.31 Å20 Å2
3---6.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30684 0 324 690 31698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.722
X-RAY DIFFRACTIONc_mcangle_it2.732.5
X-RAY DIFFRACTIONc_scbond_it2.722.5
X-RAY DIFFRACTIONc_scangle_it3.863
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 1737 5 %
Rwork0.314 33233 -
obs-35599 80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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