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- PDB-2ren: STRUCTURE OF RECOMBINANT HUMAN RENIN, A TARGET FOR CARDIOVASCULAR... -

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Basic information

Entry
Database: PDB / ID: 2ren
TitleSTRUCTURE OF RECOMBINANT HUMAN RENIN, A TARGET FOR CARDIOVASCULAR-ACTIVE DRUGS, AT 2.5 ANGSTROMS RESOLUTION
ComponentsRENIN
KeywordsHYDROLASE(ACID PROTEINASE)
Function / homology
Function and homology information


renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / amyloid-beta metabolic process / response to cAMP ...renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / response to immobilization stress / regulation of MAPK cascade / amyloid-beta metabolic process / response to cAMP / Metabolism of Angiotensinogen to Angiotensins / cell maturation / angiotensin maturation / hormone-mediated signaling pathway / insulin-like growth factor receptor binding / kidney development / regulation of blood pressure / male gonad development / cellular response to xenobiotic stimulus / apical part of cell / peptidase activity / response to lipopolysaccharide / aspartic-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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 ...Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSielecki, A.R. / James, M.N.G.
CitationJournal: Science / Year: 1989
Title: Structure of recombinant human renin, a target for cardiovascular-active drugs, at 2.5 A resolution.
Authors: Sielecki, A.R. / Hayakawa, K. / Fujinaga, M. / Murphy, M.E. / Fraser, M. / Muir, A.K. / Carilli, C.T. / Lewicki, J.A. / Baxter, J.D. / James, M.N.
History
DepositionFeb 5, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 700SHEET THE C-TERMINAL DOMAIN HAS MORE STRANDS THAT ARE NOT FORMALLY HYDROGEN BONDED TO OTHER STRANDS ...SHEET THE C-TERMINAL DOMAIN HAS MORE STRANDS THAT ARE NOT FORMALLY HYDROGEN BONDED TO OTHER STRANDS TO FORM A SHEET. THERE ARE ALSO A FEW IN THE N-TERMINAL DOMAIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4882
Polymers37,2671
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.080, 134.080, 41.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Atom site foot note1: CIS PROLINE - PRO 29 / 2: CIS PROLINE - PRO 308 / 3: CIS PROLINE - PRO 311
4: ATOMS IN THE FOLLOWING RESIDUES HAVE BEEN ASSIGNED A TEMPERATURE FACTOR OF 99.99 INDICATING THAT THE ASSOCIATED ELECTRON DENSITY IS VERY POOR: ARG 82 - GLY 86 SER 213 - THR 214 ALA 248 - ASP 254

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Components

#1: Protein RENIN


Mass: 37267.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00797, renin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY
Sequence detailsTHE HUMAN RENIN GENE HAS BEEN SEQUENCED BY TWO GROUPS: 1. HOBART ET AL. (1984) PNAS, V. 81, P. 5026 ...THE HUMAN RENIN GENE HAS BEEN SEQUENCED BY TWO GROUPS: 1. HOBART ET AL. (1984) PNAS, V. 81, P. 5026 2. HARDMAN ET AL. (1984) DNA, V. 3, P. 457 THE EXON5-EXON6 JUNCTION IN 2. HAS A 9 BASE EXON CODING FOR AN ASP-SER-GLU TRIPEPTIDE THAT IS NOT PRESENT IN 1. IN ADDITION THE C-DNA SEQUENCE OF IMAI ET AL. (1983) PNAS, V. 80, P. 7405 IS ALSO AVAILABLE AND AGREES WITH THE GENE SEQUENCE OF HARDMAN ET AL.. THE ELECTRON DENSITY MAP OF RECOMBINANT HUMAN RENIN IS EXTREMELY POOR IN THIS REGION AND THE DEPOSITORS COULD NOT RESOLVE THIS DISCREPANCY. THE COMPLETE LOOP CONTAINING THIS TRIPEPTIDE IS DISORDERED. RESIDUE NUMBERING IN THIS ENTRY AND IN THE 1989 SCIENCE PAPER FOLLOWS THE SEQUENTIAL NUMBERING DERIVED FROM THE SEQUENCE OF HARDMAN ET AL. USED IN THIS ENTRY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal grow
*PLUS
pH: 4.7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 %PEG11
250 mM11NaH2PO4-K2HPO4

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. obs: 13343 / Num. measured all: 60512 / Rmerge(I) obs: 0.48

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Processing

Software
NameClassification
X-PLORmodel building
GROMOSrefinement
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 1
Details: ATOMS IN THE FOLLOWING RESIDUES HAVE BEEN ASSIGNED A TEMPERATURE FACTOR OF 99.99 INDICATING THAT THE ASSOCIATED ELECTRON DENSITY IS VERY POOR: ARG 82 - GLY 86 SER 213 - THR 214 ALA 248 - ASP 254
RfactorNum. reflection
obs0.217 13614
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 14 0 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.03
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.71.5
X-RAY DIFFRACTIONo_mcangle_it2.82.5
X-RAY DIFFRACTIONo_scbond_it22
X-RAY DIFFRACTIONo_scangle_it3.13
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection obs: 13614 / σ(F): 1 / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_angle_d0.057

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