[English] 日本語
Yorodumi
- PDB-5vl3: CD22 d1-d3 in complex with therapeutic Fab Epratuzumab -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5vl3
TitleCD22 d1-d3 in complex with therapeutic Fab Epratuzumab
DescriptorB-cell receptor CD22
Epratuzumab Fab Heavy Chain,Epratuzumab Fab Heavy Chain
Epratuzumab Fab Light Chain,Epratuzumab Fab Light Chain
KeywordsIMMUNE SYSTEM / therapeutic antibody / Siglec / B cell / Fab
Specimen sourceHomo sapiens / human
Mus musculus / mammal / Mouse / ハツカネズミ, はつかねずみ /
MethodX-ray diffraction (3.1 Å resolution / Molecular replacement)
AuthorsSicard, T. / Ereno-Orbea, J. / Julien, J.P.
CitationNat Commun, 2017, 8, 764-764

Nat Commun, 2017, 8, 764-764 Yorodumi Papers
Molecular basis of human CD22 function and therapeutic targeting.
Ereno-Orbea, J. / Sicard, T. / Cui, H. / Mazhab-Jafari, M.T. / Benlekbir, S. / Guarne, A. / Rubinstein, J.L. / Julien, J.P.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 24, 2017 / Release: Oct 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 11, 2017Structure modelrepositoryInitial release
1.1Dec 6, 2017Structure modelDatabase referencespdbx_database_related_pdbx_database_related.content_type

-
Structure visualization

3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
Q: B-cell receptor CD22
R: B-cell receptor CD22
S: B-cell receptor CD22
T: B-cell receptor CD22
A: Epratuzumab Fab Heavy Chain
C: Epratuzumab Fab Heavy Chain
E: Epratuzumab Fab Heavy Chain
H: Epratuzumab Fab Heavy Chain
B: Epratuzumab Fab Light Chain
D: Epratuzumab Fab Light Chain
F: Epratuzumab Fab Light Chain
L: Epratuzumab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,76137
Polyers340,68812
Non-polymers5,07325
Water0
#1
Q: B-cell receptor CD22
H: Epratuzumab Fab Heavy Chain
L: Epratuzumab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,59710
Polyers85,1723
Non-polymers1,4257
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7950
ΔGint (kcal/M)-7
Surface area (Å2)35190
MethodPISA
#2
R: B-cell receptor CD22
A: Epratuzumab Fab Heavy Chain
B: Epratuzumab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4179
Polyers85,1723
Non-polymers1,2456
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7670
ΔGint (kcal/M)-10
Surface area (Å2)34560
MethodPISA
#3
S: B-cell receptor CD22
C: Epratuzumab Fab Heavy Chain
D: Epratuzumab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3299
Polyers85,1723
Non-polymers1,1576
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7530
ΔGint (kcal/M)-16
Surface area (Å2)35020
MethodPISA
#4
T: B-cell receptor CD22
E: Epratuzumab Fab Heavy Chain
F: Epratuzumab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4179
Polyers85,1723
Non-polymers1,2456
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7780
ΔGint (kcal/M)-10
Surface area (Å2)34640
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)87.110, 90.220, 136.632
Angle α, β, γ (deg.)70.83, 80.81, 80.99
Int Tables number1
Space group name H-MP 1

-
Components

-
Polypeptide(L) , 1 types, 4 molecules QRST

#1: Polypeptide(L)
B-cell receptor CD22 / B-lymphocyte cell adhesion molecule / BL-CAM / Sialic acid-binding Ig-like lectin 2 / Siglec-2 / T-cell surface antigen Leu-14


Mass: 36802.406 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens / References: UniProt: P20273

Cellular component

Molecular function

Biological process

-
Epratuzumab Fab ... , 2 types, 8 molecules ACEHBDFL

#2: Polypeptide(L)
Epratuzumab Fab Heavy Chain


Mass: 24028.684 Da / Num. of mol.: 4
Source: (gene. exp.) Mus musculus, (gene. exp.) Homo sapiens
References: UniProt: S6B291
#3: Polypeptide(L)
Epratuzumab Fab Light Chain


Mass: 24340.979 Da / Num. of mol.: 4
Source: (gene. exp.) Mus musculus, (gene. exp.) Homo sapiens
References: UniProt: Q8TCD0

-
Non-polymers , 4 types, 25 molecules

#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 16 / Formula: C8H15NO6
#5: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 4 / Formula: C6H12O6
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 4 / Formula: C6H12O6
#7: ChemicalChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Formula: C3H8O3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 / Density percent sol: 58.84
Crystal growTemp: 293 K / Method: VAPOR DIFFUSION / Details: 20 mM Tris pH 8.0 and 150 mM NaCl, 5mg/mL

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: CLSI BEAMLINE 08ID-1 / Synchrotron site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949
DetectorType: RAYONIX MX-300 / Detector: CCD / Collection date: Dec 1, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 65.68 Å2 / D resolution high: 3.1 Å / D resolution low: 39.345 Å / Number obs: 65863 / CC half: 0.987 / Rmerge I obs: 0.09 / Rpim I all: 0.09 / NetI over sigmaI: 8.2 / Redundancy: 1.9 / Percent possible obs: 94.2
Reflection shellRmerge I obs: 0.39 / Highest resolution: 3.1 Å / Lowest resolution: 3.2 Å / MeanI over sigI obs: 1.9 / CC half: 0.74 / Rpim I all: 0.39 / Redundancy: 1.9 / Percent possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XPREP2015/1data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.43 / Cross valid method: FREE R-VALUE / Sigma F: 1.96 / Overall phase error: 32.03 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2953 / R factor R work: 0.2801 / R factor obs: 0.2806 / Highest resolution: 3.1 Å / Lowest resolution: 39.345 Å / Number reflection R free: 2000 / Number reflection obs: 65847 / Percent reflection R free: 3.04 / Percent reflection obs: 94.2
Refine hist #LASTHighest resolution: 3.1 Å / Lowest resolution: 39.345 Å
Number of atoms included #LASTProtein: 22594 / Nucleic acid: 0 / Ligand: 318 / Solvent: 0 / Total: 22912
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423512
X-RAY DIFFRACTIONf_angle_d0.85332007
X-RAY DIFFRACTIONf_dihedral_angle_d14.83414083
X-RAY DIFFRACTIONf_chiral_restr0.0493634
X-RAY DIFFRACTIONf_plane_restr0.0054019
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
3.10000.33850.35783.1775146467197.00
3.17750.36620.35033.2634147469297.00
3.26340.29830.33403.3593146466096.00
3.35930.34140.32313.4677146464496.00
3.46770.33030.31843.5916144463196.00
3.59160.29990.31363.7353144458695.00
3.73530.35800.30373.9051144461295.00
3.90510.32530.28844.1108142451293.00
4.11080.32680.26354.3680140449893.00
4.36800.25180.25264.7048140444092.00
4.70480.27340.24405.1773140448092.00
5.17730.25520.25385.9243140447893.00
5.92430.30570.27617.4557143452693.00
7.45570.22870.237939.3483138441791.00

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more