[English] 日本語
Yorodumi
- PDB-2x0b: Crystal structure of human angiotensinogen complexed with renin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x0b
TitleCrystal structure of human angiotensinogen complexed with renin
Components
  • ANGIOTENSINOGENAngiotensin
  • RENIN
KeywordsHYDROLASE/HORMONE / HYDROLASE-HORMONE COMPLEX / HYDROLASE HORMONE COMPLEX / VASOCONSTRICTOR / GLYCOPROTEIN / HYPERTENSION / SERPINS / ZYMOGEN / HYDROLASE / VASOACTIVE
Function / homology
Function and homology information


regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / regulation of renal sodium excretion / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / positive regulation of activation of Janus kinase activity / renin ...regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / regulation of renal sodium excretion / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / positive regulation of activation of Janus kinase activity / renin / regulation of renal output by angiotensin / positive regulation of NAD(P)H oxidase activity / juxtaglomerular apparatus development / mesonephros development / response to cGMP / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renin-angiotensin regulation of aldosterone production / renal system process / drinking behavior / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of CoA-transferase activity / positive regulation of extracellular matrix assembly / positive regulation of macrophage derived foam cell differentiation / low-density lipoprotein particle remodeling / vasoconstriction / type 1 angiotensin receptor binding / response to angiotensin / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of gap junction assembly / regulation of MAPK cascade / regulation of vasoconstriction / response to immobilization stress / regulation of cardiac conduction / angiotensin maturation / positive regulation of epithelial to mesenchymal transition / blood vessel remodeling / positive regulation of protein tyrosine kinase activity / Metabolism of Angiotensinogen to Angiotensins / amyloid-beta metabolic process / nitric oxide mediated signal transduction / cell maturation / response to cAMP / insulin-like growth factor receptor binding / positive regulation of protein metabolic process / hormone-mediated signaling pathway / Peptide ligand-binding receptors / negative regulation of MAP kinase activity / positive regulation of endothelial cell migration / kidney development / regulation of cell growth / positive regulation of cytokine production / angiotensin-activated signaling pathway / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / PPARA activates gene expression / regulation of blood pressure / positive regulation of inflammatory response / positive regulation of miRNA transcription / male gonad development / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cellular response to xenobiotic stimulus / cell-cell signaling / apical part of cell / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / peptidase activity / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / regulation of apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / signaling receptor binding / positive regulation of DNA-templated transcription / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Angiotensinogen, serpin domain / Angiotensinogen / Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Serpin, conserved site / Serpins signature. / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Renin / Angiotensinogen
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.33 Å
AuthorsZhou, A. / Wei, Z. / Yan, Y. / Carrell, R.W. / Read, R.J.
CitationJournal: Nature / Year: 2010
Title: A Redox Switch in Angiotensinogen Modulates Angiotensin Release.
Authors: Zhou, A. / Carrell, R.W. / Murphy, M.P. / Wei, Z. / Yan, Y. / Stanley, P.L. / Stein, P.E. / Pipkin, F.B. / Read, R.J.
History
DepositionDec 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RENIN
B: ANGIOTENSINOGEN
C: RENIN
D: ANGIOTENSINOGEN
E: RENIN
F: ANGIOTENSINOGEN
G: RENIN
H: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)368,6878
Polymers368,6878
Non-polymers00
Water0
1
E: RENIN
F: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)92,1722
Polymers92,1722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-31.8 kcal/mol
Surface area30710 Å2
MethodPISA
2
C: RENIN
D: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)92,1722
Polymers92,1722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-31.7 kcal/mol
Surface area30710 Å2
MethodPISA
3
A: RENIN
B: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)92,1722
Polymers92,1722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-31.4 kcal/mol
Surface area30710 Å2
MethodPISA
4
G: RENIN
H: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)92,1722
Polymers92,1722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-30.7 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.475, 212.475, 474.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
RENIN / / ANGIOTENSINOGENASE


Mass: 42364.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-HANGT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00797, renin
#2: Protein
ANGIOTENSINOGEN / Angiotensin / SERPIN A8


Mass: 49807.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: HUMAN ANGIOTENSINOGEN / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-HANGT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01019

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 6 Å3/Da / Density % sol: 79 % / Description: NONE
Crystal growpH: 6 / Details: 1.6-2.2M AS, 0.1M MES, PH6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 31, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.35→50.5 Å / Num. obs: 6793 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 170.03 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 3.6
Reflection shellResolution: 4.35→4.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1 / % possible all: 89.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_249)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WXW

2wxw


Resolution: 4.33→48.52 Å / SU ML: 0.82 / σ(F): 1.96 / Phase error: 41.6 / Stereochemistry target values: ML
Details: STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT. VERY LIMITED REBUILDING WAS CARRIED OUT. IT WAS CLEAR FROM ELECTRON DENSITY THAT THE N-TERMINAL SUBSTRATE PORTION OF ANGIOTENSINOGEN WAS BOUND ...Details: STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT. VERY LIMITED REBUILDING WAS CARRIED OUT. IT WAS CLEAR FROM ELECTRON DENSITY THAT THE N-TERMINAL SUBSTRATE PORTION OF ANGIOTENSINOGEN WAS BOUND IN THE ACTIVE SITE. THIS WAS MODELED BY SUPERIMPOSING THE STRUCTURE OF 1SMR, CHANGING THE SIDE CHAINS AND ADJUSTING THE ROTAMERS. RESIDUES CORRESPONDING TO 3-5 AND 15- 18 OF ANGIOTENSINOGEN WERE ADDED, ROUGHLY FITTING THEM TO THE DENSITY. DIFFERENCE DENSITY AND DENSITY OBTAINED BY AVERAGING THE FOUR COPIES IN COOT MADE IT CLEAR THAT THE LOOP 127-143 OF ANGIOTENSINOGEN HAD TO CHANGE CONFORMATION TO AVOID SERIOUS CLASHES WITH RENIN. THIS LOOP WAS REBUILT TO ROUGHLY FOLLOW THE DENSITY, BUT THE DETAILS OF ITS CONFORMATION WILL NOT BE RELIABLE. THIS IS WHY THERE ARE SERIOUS CLASHES IN THIS PORTION
RfactorNum. reflection% reflection
Rfree0.334 2572 5.05 %
Rwork0.309 --
obs0.31 50950 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 197.49 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-49.3656 Å20 Å20 Å2
2--49.3656 Å20 Å2
3----98.7313 Å2
Refinement stepCycle: LAST / Resolution: 4.33→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23244 0 0 0 23244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623792
X-RAY DIFFRACTIONf_angle_d1.15832328
X-RAY DIFFRACTIONf_dihedral_angle_d17.6128344
X-RAY DIFFRACTIONf_chiral_restr0.0753728
X-RAY DIFFRACTIONf_plane_restr0.0064120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3352-4.41850.45411250.44132078X-RAY DIFFRACTION75
4.4185-4.50860.43521190.40932294X-RAY DIFFRACTION82
4.5086-4.60660.36931350.3922787X-RAY DIFFRACTION99
4.6066-4.71360.39511410.36552773X-RAY DIFFRACTION99
4.7136-4.83140.3831410.34492769X-RAY DIFFRACTION100
4.8314-4.96190.3841570.352783X-RAY DIFFRACTION99
4.9619-5.10780.37971350.3492787X-RAY DIFFRACTION99
5.1078-5.27250.37931690.33252772X-RAY DIFFRACTION99
5.2725-5.46070.37131330.33022792X-RAY DIFFRACTION99
5.4607-5.6790.32111560.30282730X-RAY DIFFRACTION99
5.679-5.9370.32071500.32162785X-RAY DIFFRACTION99
5.937-6.24940.40571430.31982784X-RAY DIFFRACTION99
6.2494-6.640.41241540.32232736X-RAY DIFFRACTION99
6.64-7.15120.33641460.32162742X-RAY DIFFRACTION98
7.1512-7.86820.32651420.28382741X-RAY DIFFRACTION98
7.8682-9.00040.30331410.25622713X-RAY DIFFRACTION97
9.0004-11.31580.24681520.20662683X-RAY DIFFRACTION96
11.3158-48.52310.2971330.3072629X-RAY DIFFRACTION94
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)
15.16425.0053-2.22937.6213-2.77563.3370.3577-0.3845-0.4134-0.2569-0.0029-0.14491.1011-0.696701.95290.0646-0.30291.5903-0.0871.9311117.0373-103.5858-1.7841
25.14580.2160.37014.2786-1.10036.43090.0438-0.4755-0.38740.44410.14350.431-0.3593-1.1626-0.00010.9956-0.1961-0.03051.7176-0.02071.84982.0066-90.8964-9.6123
35.5871-5.5433-0.13588.87351.7196-0.0182-0.4998-1.08480.40530.69050.15840.43911.1732-0.9701-0.0012.3951-0.0240.45662.116-0.04132.160276.6281-88.3169109.1534
47.51130.9809-0.95865.4891-2.55926.57-0.88240.1557-0.8324-0.15620.74250.60711.0625-1.6957-0.00012.0157-0.50410.07752.1984-0.13782.14548.5616-94.333284.2793
56.96980.54183.1253-1.13512.80664.0963-0.2547-0.0588-0.5041-0.25740.0663-0.2209-0.3670.401403.04560.2460.21542.55890.55342.5029120.5098-128.941362.8656
66.39540.015-1.74718.8607-0.90089.83610.04080.27110.2188-0.19450.24650.1752-0.24710.43830.0012.0740.0713-0.07620.84580.04731.6637109.3295-118.376197.6281
74.9357-2.9758-2.53081.7298-0.511310.7669-0.1879-0.1354-1.0216-0.35430.06480.68760.9967-0.9176-0.00112.5142-0.5914-0.02232.3862-0.23422.759652.679-105.172839.3267
88.10681.74982.13856.09412.80798.28750.17970.2743-0.78540.5874-0.19430.12211.75950.4108-0.19372.49290.07490.55320.81490.16851.930781.8897-129.528137.3738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A OR (CHAIN B AND RESSEQ 3:18)
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 31:449
3X-RAY DIFFRACTION3CHAIN C OR (CHAIN D AND RESSEQ 3:18)
4X-RAY DIFFRACTION4CHAIN D AND RESSEQ 31:449
5X-RAY DIFFRACTION5CHAIN E OR (CHAIN F AND RESSEQ 3:18)
6X-RAY DIFFRACTION6CHAIN F AND RESSEQ 31:449
7X-RAY DIFFRACTION7CHAIN G OR (CHAIN H AND RESSEQ 3:18)
8X-RAY DIFFRACTION8CHAIN H AND RESSEQ 31:449

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more