[English] 日本語
Yorodumi
- PDB-8il7: Structure of human soluble Adenylyl Cyclase in complex with lactate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8il7
TitleStructure of human soluble Adenylyl Cyclase in complex with lactate
ComponentsAdenylate cyclase type 10
KeywordsLYASE / SAC
Function / homology
Function and homology information


negative regulation of cardiac muscle cell contraction / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / astrocyte end-foot / central region of growth cone / positive regulation of glycogen catabolic process / glucose catabolic process / regulation of mitophagy ...negative regulation of cardiac muscle cell contraction / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / astrocyte end-foot / central region of growth cone / positive regulation of glycogen catabolic process / glucose catabolic process / regulation of mitophagy / regulation of membrane repolarization / adenylate cyclase / basal part of cell / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cAMP biosynthetic process / positive regulation of ossification / adenylate cyclase activity / positive regulation of protein targeting to mitochondrion / neuron projection extension / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of ATP biosynthetic process / positive regulation of mitochondrial depolarization / positive regulation of reactive oxygen species biosynthetic process / positive regulation of cardiac muscle hypertrophy / negative regulation of mitochondrial membrane potential / spermatid development / positive regulation of axon extension / Hedgehog 'off' state / positive regulation of cardiac muscle cell apoptotic process / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / cilium / manganese ion binding / ATPase binding / cytoskeleton / intracellular signal transduction / apical plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Adenylate cyclase, type 10 / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / Adenylate cyclase type 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, Q.J. / Li, Z.L. / Gao, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130057 China
CitationJournal: Cell Metab. / Year: 2023
Title: Lactate modulates iron metabolism by binding soluble adenylyl cyclase.
Authors: Liu, W. / Zhang, S. / Li, Q. / Wu, Y. / Jia, X. / Feng, W. / Li, Z. / Shi, Y. / Hou, Q. / Ma, J. / Liu, Y. / Gao, P. / Ganz, T. / Liu, S.
History
DepositionMar 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenylate cyclase type 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6365
Polymers54,2701
Non-polymers3664
Water4,576254
1
A: Adenylate cyclase type 10
hetero molecules

A: Adenylate cyclase type 10
hetero molecules

A: Adenylate cyclase type 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,90815
Polymers162,8093
Non-polymers1,09912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10060 Å2
ΔGint-44 kcal/mol
Surface area53850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.280, 99.280, 98.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Adenylate cyclase type 10 / AH-related protein / Adenylate cyclase homolog


Mass: 54269.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADCY10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96PN6, adenylate cyclase
#2: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.2 M Sodium citrate tribasic, 15% PEG 3350, 0.1 M sodium lactate pH 3.8, 10% glycerol

-
Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.95→49.64 Å / Num. obs: 40207 / % possible obs: 99.94 % / Redundancy: 14.3 % / CC1/2: 0.998 / Net I/σ(I): 20.3
Reflection shellResolution: 1.95→2.05 Å / Num. unique obs: 5705 / CC1/2: 0.857

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIX1.19.2_4158refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49.64 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 2003 4.98 %
Rwork0.1628 --
obs0.1642 40207 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 24 254 3924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143796
X-RAY DIFFRACTIONf_angle_d1.3225138
X-RAY DIFFRACTIONf_dihedral_angle_d6.466509
X-RAY DIFFRACTIONf_chiral_restr0.072567
X-RAY DIFFRACTIONf_plane_restr0.01656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.21571490.16542724X-RAY DIFFRACTION100
2-2.050.18281620.14962698X-RAY DIFFRACTION100
2.05-2.110.20291210.15582729X-RAY DIFFRACTION100
2.11-2.180.23781540.15682692X-RAY DIFFRACTION100
2.18-2.260.19121360.1542749X-RAY DIFFRACTION100
2.26-2.350.20061380.15522716X-RAY DIFFRACTION100
2.35-2.460.18351470.15412725X-RAY DIFFRACTION100
2.46-2.590.22871390.16192723X-RAY DIFFRACTION100
2.59-2.750.19451100.16972770X-RAY DIFFRACTION100
2.75-2.960.20431560.17462701X-RAY DIFFRACTION100
2.96-3.260.16651290.16782753X-RAY DIFFRACTION100
3.26-3.730.17381510.15452725X-RAY DIFFRACTION100
3.73-4.70.14831610.14242739X-RAY DIFFRACTION100
4.7-49.640.22111500.19482760X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -32.347 Å / Origin y: 6.573 Å / Origin z: 0.4007 Å
111213212223313233
T0.173 Å20.0124 Å2-0.0098 Å2-0.1166 Å20.0102 Å2--0.1755 Å2
L0.4933 °2-0.0008 °20.0018 °2-0.5356 °20.4027 °2--1.1594 °2
S0.0085 Å °-0.002 Å °-0.1165 Å °0.0827 Å °-0.0111 Å °-0.0503 Å °0.2683 Å °0.0723 Å °0.0043 Å °
Refinement TLS groupSelection details: all

+
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