[English] 日本語
Yorodumi
- PDB-4f45: Crystal structure of human CD38 E226Q mutant in complex with NAADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f45
TitleCrystal structure of human CD38 E226Q mutant in complex with NAADP
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / CD38 / ADP-ribosyl cyclase / NAADP / Calcium signaling
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / artery smooth muscle contraction / Nicotinate metabolism / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD metabolic process / NAD+ nucleotidase, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to hydroperoxide / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / positive regulation of vasoconstriction / response to interleukin-1 / apoptotic signaling pathway / response to progesterone / female pregnancy / B cell receptor signaling pathway / positive regulation of insulin secretion / negative regulation of neuron projection development / response to estradiol / positive regulation of cytosolic calcium ion concentration / transferase activity / positive regulation of cell growth / basolateral plasma membrane / nuclear membrane / response to hypoxia / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
ADP Ribosyl Cyclase; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DN4 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsZhang, H. / Lee, H.C. / Hao, Q.
CitationJournal: MESSENGER / Year: 2013
Title: Crystal Structures of Human CD38 in Complex with NAADP and ADPRP
Authors: Zhang, H. / Graeff, R. / Lee, H.C. / Hao, Q.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1124
Polymers59,6242
Non-polymers1,4892
Water1,58588
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5562
Polymers29,8121
Non-polymers7441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5562
Polymers29,8121
Non-polymers7441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.694, 54.565, 63.420
Angle α, β, γ (deg.)109.670, 91.110, 93.680
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein ADP-ribosyl cyclase 1 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10


Mass: 29811.754 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 46-300 / Mutation: Q49T, N100D, N164A, N209D, N219D, E226Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical ChemComp-DN4 / [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(3-carboxypyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate / Nicotinic acid adenine dinucleotide phosphate


Mass: 744.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N6O18P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.86 % / Mosaicity: 0.744 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium acetate pH 4.0, 12% PEG 20K, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: MX225 / Detector: CCD / Date: Dec 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28795 / % possible obs: 94 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Χ2: 1.37 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.182.90.26623750.924177.8
2.18-2.263.10.21925631.141183.5
2.26-2.373.30.18128151.012191.5
2.37-2.493.50.14529391.047196.6
2.49-2.653.70.11630141.151198.2
2.65-2.853.90.10230191.196198.4
2.85-3.1440.07830031.302198.2
3.14-3.5940.06330341.621198.9
3.59-4.523.90.05430381.977199.2
4.52-503.80.04729951.888197.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2415 / WRfactor Rwork: 0.1826 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8413 / SU B: 11.561 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2363 / SU Rfree: 0.1938 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1448 5 %RANDOM
Rwork0.1707 ---
obs0.1735 28791 93.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 167.2 Å2 / Biso mean: 61.2542 Å2 / Biso min: 23.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å2-0.96 Å21.34 Å2
2--2.16 Å20.97 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 96 88 4217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024251
X-RAY DIFFRACTIONr_bond_other_d0.0010.022917
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9645786
X-RAY DIFFRACTIONr_angle_other_deg0.853.0087004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8524.158202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57515724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8211526
X-RAY DIFFRACTIONr_chiral_restr0.1420.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02866
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 80 -
Rwork0.237 1577 -
all-1657 -
obs--73.58 %
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)
15.86771.1464-1.86322.5708-1.10046.41220.1813-0.210.7658-0.0847-0.0666-0.027-0.61860.2732-0.11470.12580.01770.02750.07120.0160.1908-399.546-918.6389.387
23.09710.0953-3.6086.45985.097810.313-0.30170.72530.0617-0.24150.4693-0.27830.3638-0.3681-0.16750.1851-0.01420.01460.36160.15220.204-399.818-928.472-6.475
36.42931.1028-3.86741.3266-1.29469.98130.0547-0.39860.0275-0.1201-0.00330.04760.04650.0833-0.05140.05060.0331-0.01180.11750.05030.1077-402.179-925.7629.524
49.3174-0.6809-3.0866.5717-1.31278.847-0.89050.4838-0.29050.07030.60590.04581.5507-1.28070.28470.5151-0.2343-0.00150.3159-0.00690.0671-407.471-938.315-5.207
511.0310.4456-4.18138.2976-2.39966.3755-0.8269-0.0778-1.6677-0.1659-0.1275-0.55352.2961-0.29150.95441.0308-0.06660.19790.2488-0.07720.3229-400.771-946.951-9.429
616.2188-1.85281.80113.058-0.22884.49590.29650.6598-2.2073-0.0187-0.16050.46920.5048-0.1637-0.13610.2070.0056-0.04960.1163-0.12220.4015-418.185-954.22726.418
74.2514-0.7579-0.04776.31160.43941.11620.04170.3885-0.34220.22440.12520.19860.15350.1679-0.1670.06520.037-0.0230.35250.01880.0789-427.18-938.7528.117
813.5748-3.86381.84094.273-1.68472.665-0.1625-0.2901-1.13180.2290.19630.18570.13950.041-0.03370.1864-0.0219-0.00210.16990.01340.106-417.9-949.1129.537
94.2585-3.2404-0.39865.3111-0.97971.6809-0.00490.33960.20360.0041-0.0324-0.27810.06390.06840.03730.0554-0.0494-0.02110.25790.02730.0339-416.97-937.73426.187
106.3881.6509-3.10074.0632-0.73385.95140.374-0.47420.75210.6643-0.14520.1338-0.25130.1761-0.22870.1620.02320.00980.2135-0.03410.1219-424.395-924.60633.155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 106
2X-RAY DIFFRACTION2A107 - 140
3X-RAY DIFFRACTION3A141 - 193
4X-RAY DIFFRACTION4A194 - 243
5X-RAY DIFFRACTION5A244 - 291
6X-RAY DIFFRACTION6B45 - 107
7X-RAY DIFFRACTION7B108 - 138
8X-RAY DIFFRACTION8B139 - 176
9X-RAY DIFFRACTION9B177 - 210
10X-RAY DIFFRACTION10B211 - 296

+
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