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- PDB-1smr: The 3-d structure of mouse submaxillary renin complexed with a de... -

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Basic information

Entry
Database: PDB / ID: 1smr
TitleThe 3-d structure of mouse submaxillary renin complexed with a decapeptide inhibitor ch-66 based on the 4-16 fragment of rat angiotensinogen
Components
  • INHIBITOR CH-66
  • RENIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTIC PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure / negative regulation of tissue remodeling / uterine smooth muscle contraction / positive regulation of L-lysine import across plasma membrane / establishment of blood-nerve barrier / positive regulation of L-arginine import across plasma membrane / aldosterone secretion / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system ...renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure / negative regulation of tissue remodeling / uterine smooth muscle contraction / positive regulation of L-lysine import across plasma membrane / establishment of blood-nerve barrier / positive regulation of L-arginine import across plasma membrane / aldosterone secretion / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / ovarian follicle rupture / regulation of transmission of nerve impulse / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / Metabolism of Angiotensinogen to Angiotensins / negative regulation of neurotrophin TRK receptor signaling pathway / positive regulation of extracellular matrix constituent secretion / Peptide ligand-binding receptors / vasopressin secretion / cell growth involved in cardiac muscle cell development / regulation of extracellular matrix assembly / operant conditioning / renin / vascular associated smooth muscle cell proliferation / regulation of renal output by angiotensin / regulation of norepinephrine secretion / artery smooth muscle contraction / response to cGMP / renin-angiotensin regulation of aldosterone production / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / renal system process / drinking behavior / peristalsis / positive regulation of macrophage derived foam cell differentiation / positive regulation of organ growth / positive regulation of extracellular matrix assembly / smooth muscle cell differentiation / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of fatty acid biosynthetic process / positive regulation of blood pressure / intracellular sodium ion homeostasis / positive regulation of multicellular organism growth / vasoconstriction / type 1 angiotensin receptor binding / hormone metabolic process / cellular response to angiotensin / response to angiotensin / positive regulation of vascular associated smooth muscle cell migration / positive regulation of extrinsic apoptotic signaling pathway / G alpha (q) signalling events / G alpha (i) signalling events / positive regulation of epidermal growth factor receptor signaling pathway / organ growth / branching involved in ureteric bud morphogenesis / positive regulation of cardiac muscle cell apoptotic process / blood vessel development / positive regulation of cardiac muscle hypertrophy / negative regulation of vascular associated smooth muscle cell proliferation / associative learning / regulation of calcium ion transport / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of cardiac conduction / angiotensin maturation / positive regulation of epithelial to mesenchymal transition / positive regulation of insulin receptor signaling pathway / stress-activated MAPK cascade / response to mechanical stimulus / response to salt stress / response to cAMP / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / positive regulation of protein metabolic process / ERK1 and ERK2 cascade / positive regulation of endothelial cell migration / regulation of heart rate / response to cold / extracellular matrix organization / negative regulation of angiogenesis / cell-matrix adhesion / positive regulation of superoxide anion generation / positive regulation of cytokine production / kidney development / angiotensin-activated signaling pathway / female pregnancy / astrocyte activation / negative regulation of smooth muscle cell proliferation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / negative regulation of cell growth / hormone activity / positive regulation of miRNA transcription / regulation of blood pressure / positive regulation of neuron projection development / cellular response to mechanical stimulus / vasodilation / protein import into nucleus / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 ...Angiotensinogen, serpin domain / Angiotensinogen / Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Renin-2 / Angiotensinogen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDealwis, C.G. / Blundell, T.L.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: X-ray analysis at 2.0 A resolution of mouse submaxillary renin complexed with a decapeptide inhibitor CH-66, based on the 4-16 fragment of rat angiotensinogen.
Authors: Dealwis, C.G. / Frazao, C. / Badasso, M. / Cooper, J.B. / Tickle, I.J. / Driessen, H. / Blundell, T.L. / Murakami, K. / Miyazaki, H. / Sueiras-Diaz, J. / Szelke, M.J.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary X-Ray Analysis of Complexes of Peptide Inhibitors with Human Recombinant and Mouse Submandibular Renins
Authors: Badasso, M. / Frazao, C. / Sibanda, B.L. / Dhanaraj, V. / Dealwis, C. / Cooper, J.B. / Wood, S.P. / Blundell, T.L. / Murakami, K. / Miyazaki, H. / Hobart, P.M. / Geoghegan, K.F. / Ammirati, ...Authors: Badasso, M. / Frazao, C. / Sibanda, B.L. / Dhanaraj, V. / Dealwis, C. / Cooper, J.B. / Wood, S.P. / Blundell, T.L. / Murakami, K. / Miyazaki, H. / Hobart, P.M. / Geoghegan, K.F. / Ammirati, M.J. / Lanzetti, A.J. / Danley, D.E. / O'Connor, B.A. / Hoover, D.J. / Sueiras-Diaz, J. / Jones, D.M. / Szelke, M.
#2: Journal: Nature / Year: 1992
Title: X-Ray Analysis of Peptide-Inhibitor Complexes Define the Structure Basis of Specificity for Human and Mouse Renins
Authors: Dhanaraj, V. / Dealwis, C.G. / Frazao, C. / Badasso, M. / Sibanda, B.L. / Tickle, I.J. / Cooper, J.B. / Driessen, H.P.C. / Newman, M. / Aguilar, C. / Wood, S.P. / Blundell, T.L. / Hobart, P. ...Authors: Dhanaraj, V. / Dealwis, C.G. / Frazao, C. / Badasso, M. / Sibanda, B.L. / Tickle, I.J. / Cooper, J.B. / Driessen, H.P.C. / Newman, M. / Aguilar, C. / Wood, S.P. / Blundell, T.L. / Hobart, P.M. / Geoghegan, K.F. / Ammirati, M.J. / Danley, D.E. / O'Connor, B.A.O. / Hoover, D.J.
History
DepositionMar 11, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RENIN
B: INHIBITOR CH-66
C: RENIN
D: INHIBITOR CH-66
E: RENIN
F: INHIBITOR CH-66
G: RENIN
H: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)151,1878
Polymers151,1878
Non-polymers00
Water2,810156
1
A: RENIN
B: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)37,7972
Polymers37,7972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-12 kcal/mol
Surface area13570 Å2
MethodPISA
2
C: RENIN
D: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)37,7972
Polymers37,7972
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-12 kcal/mol
Surface area13560 Å2
MethodPISA
3
E: RENIN
F: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)37,7972
Polymers37,7972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-12 kcal/mol
Surface area13570 Å2
MethodPISA
4
G: RENIN


Theoretical massNumber of molelcules
Total (without water)36,5331
Polymers36,5331
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
H: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)1,2631
Polymers1,2631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
A: RENIN
B: INHIBITOR CH-66

C: RENIN
D: INHIBITOR CH-66

E: RENIN
F: INHIBITOR CH-66

G: RENIN
H: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)151,1878
Polymers151,1878
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
crystal symmetry operation1_453x-1,y,z-21
crystal symmetry operation1_464x-1,y+1,z-11
Buried area17250 Å2
ΔGint-86 kcal/mol
Surface area46120 Å2
MethodPISA
7
A: RENIN
B: INHIBITOR CH-66

C: RENIN
D: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)75,5944
Polymers75,5944
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
Buried area6520 Å2
ΔGint-33 kcal/mol
Surface area25170 Å2
MethodPISA
8
E: RENIN
F: INHIBITOR CH-66

G: RENIN
H: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)75,5944
Polymers75,5944
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_566x,y+1,z+11
Buried area6450 Å2
ΔGint-33 kcal/mol
Surface area25230 Å2
MethodPISA
9
G: RENIN
H: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)37,7972
Polymers37,7972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-12 kcal/mol
Surface area13560 Å2
MethodPISA
10
A: RENIN

C: RENIN

E: RENIN

G: RENIN


Theoretical massNumber of molelcules
Total (without water)146,1334
Polymers146,1334
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
crystal symmetry operation1_453x-1,y,z-21
crystal symmetry operation1_464x-1,y+1,z-11
Buried area7460 Å2
ΔGint-38 kcal/mol
Surface area49220 Å2
MethodPISA
11
B: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)1,2631
Polymers1,2631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
D: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)1,2631
Polymers1,2631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
F: INHIBITOR CH-66


Theoretical massNumber of molelcules
Total (without water)1,2631
Polymers1,2631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.340, 117.760, 85.880
Angle α, β, γ (deg.)90.00, 101.18, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES PRO A 23, PRO A 111, PRO A 294, AND PRO A 297 ARE CIS PROLINES.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9049, -0.1925, 0.3796), (-0.1958, -0.9802, -0.0303), (0.3779, -0.0469, -0.9247)11.955, 69.001, 36.4885
2given(-0.9855, 0.1694, -0.0037), (0.1692, 0.9852, 0.0287), (0.0085, 0.0276, -0.9996)90.955, -3.358, 123.76
3given(-0.9235, 0.0485, -0.3805), (-0.0516, -0.9987, -0.0022), (-0.3801, 0.0176, 0.9248)108.283, 67.075, 92.871

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Components

#1: Protein
RENIN


Mass: 36533.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CDNA / Plasmid: CLASSIFIED / References: UniProt: P00796, renin
#2: Protein/peptide
INHIBITOR CH-66


Mass: 1263.482 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
References: UniProt: P01015*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INHIBITOR CH-66 IS BASED ON THE 6-14 FRAGMENT OF RAT ANGIOTENSINOGEN AND HAS THE FORMULA PIV- ...THE INHIBITOR CH-66 IS BASED ON THE 6-14 FRAGMENT OF RAT ANGIOTENSINOGEN AND HAS THE FORMULA PIV-HIS6-PRO-PHE-HIS-LEU-OH-LEU-TYR-TYR-SER14-NH2, WHERE PIV IS A PIVALOYL GROUP AND -OH DENOTES A HYDROXYETHYLENE (-CHOH-CH=2=-) TRANSITION-STATE ISOSTERE OF THE SCISSILE BOND. ALL CHIRAL CENTERS, INCLUDING THOSE OF THE ISOSTERE, ARE OF THE S-FORM. T12 - T16 OF THE TURN RECORD BELOW DO NOT FORM I TO I+3 H-BONDS. ALL BETA-HAIRPIN TURNS ARE CLASSIFIED ACCORDING TO SIBANDA ET AL., 1989, AND THE REST OF THE REVERSE TURNS ARE CLASSIFIED ACCORDING TO KABSCH AND SANDER 1983.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal grow
*PLUS
pH: 5.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.01 Msodium acetate11
210 mg/mlprotein11
310-35 %(w/v)PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 96300 / % possible obs: 94.4 % / Num. measured all: 300600 / Rmerge(I) obs: 0.109

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.18 / Highest resolution: 2 Å
Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE ...Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION - B = 8 * (PI)**2 * U**2.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10404 0 0 156 10560
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.026
X-RAY DIFFRACTIONp_angle_d0.054
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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