[English] 日本語
Yorodumi
- PDB-3i9n: Crystal structure of human CD38 complexed with an analog ribo-2'F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i9n
TitleCrystal structure of human CD38 complexed with an analog ribo-2'F-ADP ribose
ComponentsADP-ribosyl cyclase 1
KeywordsHYDROLASE / Enzyme-analog complex / covalent reaction intermediate / Alpha helices rich domain and alpha/beta domain / Diabetes mellitus / Disulfide bond / Glycoprotein / Membrane / NAD / Receptor / Signal-anchor / Transmembrane
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-AVW / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLiu, Q. / Graeff, R. / Kriksunov, I.A. / Jiang, H. / Zhang, B. / Oppenheimer, N. / Lin, H. / Potter, B.V.L. / Lee, H.C. / Hao, Q.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis for enzymatic evolution from a dedicated ADP-ribosyl cyclase to a multifunctional NAD hydrolase
Authors: Liu, Q. / Graeff, R. / Kriksunov, I.A. / Jiang, H. / Zhang, B. / Oppenheimer, N. / Lin, H. / Potter, B.V.L. / Lee, H.C. / Hao, Q.
History
DepositionJul 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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)61,8514
Polymers60,7612
Non-polymers1,0912
Water3,495194
1
A: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9262
Polymers30,3801
Non-polymers5451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosyl cyclase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9262
Polymers30,3801
Non-polymers5451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.977, 54.371, 64.258
Angle α, β, γ (deg.)109.82, 90.92, 94.86
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein ADP-ribosyl cyclase 1 / CD38 / Cyclic ADP-ribose hydrolase 1 / cADPr hydrolase 1 / T10


Mass: 30380.393 Da / Num. of mol.: 2
Fragment: extracellular domain, enzymatic domain, residues 45-300
Mutation: Q49T, N100D, N164D, N209D, N219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD38 / Plasmid: PPICZ(ALPHA)A / Production host: Pichia Pastoris (fungus) / Strain (production host): X-33 (INVITROGEN) / References: UniProt: P28907, NAD+ glycohydrolase
#2: Chemical ChemComp-AVW / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4S)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / ribosyl-2-fluoro-deoxy-adenosine diphosphate ribose / ribo-2'F-ADPR


Mass: 545.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22FN5O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES, pH 6.0, 15% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 17, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 33891 / Num. obs: 33891 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 95.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YH3

1yh3


Resolution: 2.01→27.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.076 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.246 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 1705 5.1 %RANDOM
Rwork0.21316 31737 --
all0.21624 ---
obs0.21624 33442 94.77 %-
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: 98.65 Å2 / Biso mean: 34.095 Å2 / Biso min: 14.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.01 Å20 Å2
2--0.04 Å2-0.01 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.01→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 70 194 4364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224290
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9555832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06924.038208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89815742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6251530
X-RAY DIFFRACTIONr_chiral_restr0.1220.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213224
X-RAY DIFFRACTIONr_mcbond_it0.9781.52522
X-RAY DIFFRACTIONr_mcangle_it1.70124114
X-RAY DIFFRACTIONr_scbond_it3.1831768
X-RAY DIFFRACTIONr_scangle_it4.8114.51718
LS refinement shellResolution: 2.012→2.064 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 128 -
Rwork0.279 2018 -
all-2146 -
obs--83.5 %
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)
112.3788-1.23064.48512.8314-1.04424.31760.4726-0.5853-1.59270.2682-0.0930.19150.4283-0.1825-0.37960.0719-0.0176-0.0121-0.08920.04520.08023.172-15.7133.921
23.8242-3.5203-0.05353.7285-0.24770.70640.28010.6674-0.6524-0.4016-0.25520.41810.2093-0.0893-0.02490.05020.0333-0.04480.0119-0.15450.03790.461-10.446-8.717
32.00341.4823-3.77787.66281.06029.38790.0685-0.2417-0.39210.3252-0.27190.730.2827-0.49620.20340.00240.02240.0438-0.1078-0.0295-0.1025-8.3743.3395.19
47.9966-0.87461.24363.9659-1.66632.94880.1549-0.143-0.69270.0553-0.1342-0.28390.05520.187-0.0207-0.06580.0020.0031-0.1475-0.0489-0.0968.565-9.1790.367
54.20180.44560.55635.01930.09764.53720.1112-0.30850.18260.4711-0.0601-0.1043-0.19840.229-0.0511-0.0888-0.01780.0191-0.1094-0.0052-0.1428-0.70714.641.625
616.63158.5858-6.854612.9487-0.88325.4384-0.4277-0.5437-0.5090.18890.10480.38010.2512-0.25660.3230.13960.04310.02890.1240.0048-0.0766-16.5812.00814.748
72.88110.1641-0.65771.9074-1.10484.0660.05040.15030.3594-0.0485-0.03710.0183-0.31990.0104-0.0133-0.08670.0146-0.0051-0.1656-0.0378-0.1119.9921.709-20.507
88.67951.06450.04344.0272-1.79228.3161-0.1406-0.59350.0762-0.1386-0.1791-0.37940.18630.34810.3197-0.058-0.00490.013-0.0683-0.0728-0.121523.5136.53-35.874
93.70490.7876-0.51251.5418-0.53746.929-0.0099-0.0295-0.0972-0.041800.0960.0568-0.09640.0099-0.1460.0350.0025-0.21780.0003-0.119419.16814.033-19.992
105.5491-1.4435-0.7166.1558-0.86944.4285-0.2605-0.2407-0.33240.15340.20150.14210.2322-0.17210.059-0.028-0.06050.0146-0.0507-0.0239-0.094614.5751.077-34.339
1123.86-8.3898-10.554519.86711.69354.9095-0.5194-0.98490.70880.37630.14180.17370.69250.69910.37760.266-0.00030.13360.09980.00060.217320.275-14.3-35.049
129.17740.2327-0.4284.0280.86431.4115-0.4171.0013-0.7112-0.22020.103-0.42880.40330.0590.31390.16940.02940.05330.0332-0.0277-0.009721.792-3.906-41.545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 75
2X-RAY DIFFRACTION2A76 - 121
3X-RAY DIFFRACTION3A122 - 145
4X-RAY DIFFRACTION4A146 - 193
5X-RAY DIFFRACTION5A194 - 275
6X-RAY DIFFRACTION6A276 - 296
7X-RAY DIFFRACTION7B45 - 116
8X-RAY DIFFRACTION8B117 - 138
9X-RAY DIFFRACTION9B139 - 193
10X-RAY DIFFRACTION10B194 - 247
11X-RAY DIFFRACTION11B248 - 259
12X-RAY DIFFRACTION12B260 - 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