[English] 日本語
Yorodumi
- PDB-3raj: Crystal structure of human CD38 in complex with the Fab fragment ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3raj
TitleCrystal structure of human CD38 in complex with the Fab fragment of antibody HB7
Components
  • ADP-ribosyl cyclase 1
  • heavy chain of the Fab fragment of antibody HB7
  • light chain of the Fab fragment of antibody HB7
KeywordsHYDROLASE/IMMUNE SYSTEM / CD38 / ADP-ribosyl cyclase / cyclic ADP-ribose / X-crystallography / Calcium signaling / agonistic antibody / HB7 / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / response to hydroperoxide ...2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase / phosphorus-oxygen lyase activity / Nicotinate metabolism / artery smooth muscle contraction / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ metabolic process / NAD+ nucleosidase activity, cyclic ADP-ribose generating / long-term synaptic depression / negative regulation of bone resorption / response to hydroperoxide / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / positive regulation of vasoconstriction / B cell proliferation / response to retinoic acid / positive regulation of B cell proliferation / response to interleukin-1 / response to progesterone / B cell receptor signaling pathway / apoptotic signaling pathway / female pregnancy / positive regulation of insulin secretion / response to estradiol / negative regulation of neuron projection development / transferase activity / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / nuclear membrane / basolateral plasma 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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold ...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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.044 Å
AuthorsZhang, H. / Lee, H.C. / Hao, Q.
CitationJournal: To be Published
Title: Engineering a novel cytosolic form of CD38 for cyclic ADP-ribose dependent signaling
Authors: Zhang, H. / Zhao, Y.J. / Hao, Q. / Lee, H.C.
History
DepositionMar 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-ribosyl cyclase 1
H: heavy chain of the Fab fragment of antibody HB7
L: light chain of the Fab fragment of antibody HB7


Theoretical massNumber of molelcules
Total (without water)76,6943
Polymers76,6943
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.664, 271.521, 136.661
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 29812.738 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 46-300 / Mutation: Q49T, N100D, N164D, N209D, N219D
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: Antibody heavy chain of the Fab fragment of antibody HB7


Mass: 23628.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell / Production host: Mus musculus (house mouse)
#3: Antibody light chain of the Fab fragment of antibody HB7


Mass: 23252.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell / Production host: Mus musculus (house mouse)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.91 % / Mosaicity: 1.003 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.6M sodium formate, pH 7.0, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97908 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 3.044→50 Å / Num. obs: 19878 / % possible obs: 92.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.085 / Χ2: 2.323 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.05-3.164.50.44515421.09472.5
3.16-3.295.10.33517381.25382.4
3.29-3.435.50.26118521.5188.1
3.43-3.625.80.20519251.75390.5
3.62-3.845.80.15819842.06593.6
3.84-4.145.80.12620742.42896.9
4.14-4.565.70.10121312.83499.3
4.56-5.215.80.08421513.09999.8
5.21-6.575.70.08221923.09799.9
6.57-505.30.04422892.97899.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_378refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YH3

1yh3


Resolution: 3.044→48.157 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7539 / SU ML: 0.38 / σ(F): 0.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.275 1001 5.06 %
Rwork0.2049 --
obs0.2084 19773 90.5 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 219.13 Å2 / Biso mean: 98.38 Å2 / Biso min: 20.73 Å2
Baniso -1Baniso -2Baniso -3
1-6.6805 Å2-0 Å20 Å2
2---10.4569 Å2-0 Å2
3---32.8916 Å2
Refinement stepCycle: LAST / Resolution: 3.044→48.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 0 0 5034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015164
X-RAY DIFFRACTIONf_angle_d1.3557015
X-RAY DIFFRACTIONf_chiral_restr0.087793
X-RAY DIFFRACTIONf_plane_restr0.006889
X-RAY DIFFRACTIONf_dihedral_angle_d16.5551833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0438-3.20420.3721020.28591956205867
3.2042-3.40490.36221390.27742455259484
3.4049-3.66780.31031440.23972628277290
3.6678-4.03670.28231530.19252752290594
4.0367-4.62040.2751590.17812908306798
4.6204-5.81960.24851450.18822977312299
5.8196-48.1630.24751590.20143096325599

+
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