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- PDB-1rne: THE CRYSTAL STRUCTURE OF RECOMBINANT GLYCOSYLATED HUMAN RENIN ALO... -

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Basic information

Entry
Database: PDB / ID: 1rne
TitleTHE CRYSTAL STRUCTURE OF RECOMBINANT GLYCOSYLATED HUMAN RENIN ALONE AND IN COMPLEX WITH A TRANSITION STATE ANALOG INHIBITOR
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 / cellular response to xenobiotic stimulus / male gonad development / 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: 2.4 Å
AuthorsGruetter, M.G. / Rahuel, J. / Priestle, J.P.
Citation
Journal: J.Struct.Biol. / Year: 1991
Title: The crystal structures of recombinant glycosylated human renin alone and in complex with a transition state analog inhibitor.
Authors: Rahuel, J. / Priestle, J.P. / Grutter, M.G.
#1: Journal: Science / Year: 1989
Title: Structure of Recombinant Human Renin, a Target for Cardiovascular-Active Drugs, at 2.5 Angstroms Resolution
Authors: Sielecki, A.R. / Hayakawa, K. / Fujinaga, M. / Murphy, M.E.P. / Fraser, M. / Muir, A.K. / Carilli, C.T. / Lewicki, J.A. / Baxter, J.D. / James, M.N.G.
#2: Journal: Embo J. / Year: 1989
Title: High-Resolution X-Ray Diffraction Study of the Complex between Endothiapepsin and an Oligopeptide Inhibitor: The Analysis of the Inhibitor Binding and Description of the Rigid Body Shift in the Enzyme
Authors: Sali, A. / Veerapandian, B. / Cooper, J.B. / Foundling, S.I. / Hoover, D.J. / Blundell, T.L.
History
DepositionDec 12, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 2.0Oct 21, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_chem_comp_identifier.comp_id / _pdbx_chem_comp_identifier.identifier / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2183
Polymers37,2671
Non-polymers9512
Water2,486138
1
A: RENIN
hetero molecules

A: RENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4366
Polymers74,5342
Non-polymers1,9024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)90.900, 90.900, 109.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: RESIDUES PRO 23, PRO 111, PRO 294, AND PRO 297 ARE CIS PROLINES.
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

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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) / Organ: OVARY / 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
#3: Chemical ChemComp-C60 / [[[3-(2-METHYL-PROPANE-2-SULFONYL)-1-BENZENYL]-2-PROPYL]-CARBONYL-HISTIDYL]-AMINO-[CYCLOHEXYLMETHYL]-[2-HYDROXY-4-ISOPROPYL]-PENTAN-5-OIC ACID BUTYLAMIDE


Mass: 730.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H63N5O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE ATOMS OF NAG 345 WERE ASSIGNED OCCUPANCIES OF 0.5 TO KEEP B-FACTORS FROM GOING OVER 100 ...THE ATOMS OF NAG 345 WERE ASSIGNED OCCUPANCIES OF 0.5 TO KEEP B-FACTORS FROM GOING OVER 100 ANGSTROMS SQUARED. THE INHIBITOR CGP 38'560 IS A TRANSITION-STATE ANALOGUE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal grow
*PLUS
pH: 3 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.3 mg/mlrenin1drop
23 mg/mlinhibitor1drop
31.1-1.3 Mammonium sulfate1reservoir
4100 mMsodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 18418 / % possible obs: 99 % / Num. measured all: 57856 / Rmerge(I) obs: 0.078

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Processing

Software
NameClassification
X-PLORmodel building
CORELSrefinement
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.176 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 65 138 2713
Software
*PLUS
Name: CORELS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg3

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