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- PDB-3vcm: Crystal structure of human prorenin -

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Basic information

Entry
Database: PDB / ID: 3vcm
TitleCrystal structure of human prorenin
Components(prorenin) x 2
KeywordsHYDROLASE / aspartic proteases / prorenin receptor
Function / homology
Function and homology information


renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / amyloid-beta metabolic process ...renin / juxtaglomerular apparatus development / mesonephros development / response to cGMP / renin-angiotensin regulation of aldosterone production / drinking behavior / regulation of MAPK cascade / response to immobilization stress / angiotensin maturation / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / cell maturation / response to cAMP / insulin-like growth factor receptor binding / hormone-mediated signaling pathway / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsMorales, R. / Watier, Y. / Bocskei, Z.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Human Prorenin Structure Sheds Light on a Novel Mechanism of Its Autoinhibition and on Its Non-Proteolytic Activation by the (Pro)renin Receptor.
Authors: Morales, R. / Watier, Y. / Bocskei, Z.
History
DepositionJan 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / software
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prorenin
B: prorenin
P: prorenin
Q: prorenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8945
Polymers83,6734
Non-polymers2211
Water1,74797
1
A: prorenin
P: prorenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0583
Polymers41,8372
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-27 kcal/mol
Surface area15850 Å2
MethodPISA
2
B: prorenin
Q: prorenin


Theoretical massNumber of molelcules
Total (without water)41,8372
Polymers41,8372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-16 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.420, 104.420, 237.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein prorenin / / Angiotensinogenase


Mass: 36721.508 Da / Num. of mol.: 2 / Fragment: renin (UNP residues 67-406)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P00797, renin
#2: Protein/peptide prorenin / / Angiotensinogenase


Mass: 5115.053 Da / Num. of mol.: 2 / Fragment: activation peptide (UNP residues 24-66)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P00797, renin
#3: 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 / N-Acetylglucosamine


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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5 M sodium malonate, 0.1 M Bis-Tris-propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.93→50 Å / Num. obs: 29148 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 61.96 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 12.1
Reflection shellResolution: 2.93→3.09 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4176 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
BUSTER2.9.7refinement
MOSFLMdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→36.53 Å / Cor.coef. Fo:Fc: 0.8729 / Cor.coef. Fo:Fc free: 0.8289 / SU R Cruickshank DPI: 0.599 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.634 / SU Rfree Blow DPI: 0.321 / SU Rfree Cruickshank DPI: 0.322
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 1476 5.08 %RANDOM
Rwork0.2118 ---
obs0.2136 29067 99.98 %-
Displacement parametersBiso mean: 48.32 Å2
Baniso -1Baniso -2Baniso -3
1--11.1356 Å20 Å20 Å2
2---11.1356 Å20 Å2
3---22.2712 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: LAST / Resolution: 2.93→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5627 0 14 97 5738
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1950SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes842HARMONIC5
X-RAY DIFFRACTIONt_it5770HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion764SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6318SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5770HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7806HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion22.7
LS refinement shellResolution: 2.93→3.03 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.294 148 5.28 %
Rwork0.2545 2655 -
all0.2566 2803 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.47440.5210.01570.7140.37470.9615-0.0312-0.0614-0.0185-0.02210.0735-0.0177-0.21110.1151-0.0423-0.02190.0184-0.0366-0.0894-0.0279-0.029-39.0214-0.265320.4044
20.5717-0.44820.66670.5675-0.5781.40260.03040.0797-0.055-0.01840.04440.04840.07980.1624-0.0748-0.13760.00280.0087-0.0122-0.0372-0.0118-27.5469-35.9114-0.0196
30.0377-0.02811.0390.61570.44830-0.0096-0.03040.00660.01550.0221-0.0069-0.020.0183-0.0125-0.0112-0.0377-0.0117-0.0371-0.0112-0.0105-35.2323-7.28112.5998
40.2673-0.13750.70990.38810.09040.2663-0.00710.00910.0008-0.00130.017-0.0028-0.02350.0192-0.0098-0.03610.03380.0033-0.0011-0.0196-0.0094-26.2546-26.54075.2329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-5 - 401
2X-RAY DIFFRACTION2{ B|* }B4 - 326
3X-RAY DIFFRACTION3{ P|* }P6 - 43
4X-RAY DIFFRACTION4{ Q|* }Q6 - 30

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