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- PDB-5vl3: CD22 d1-d3 in complex with therapeutic Fab Epratuzumab -

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Basic information

Entry
Database: PDB / ID: 5vl3
TitleCD22 d1-d3 in complex with therapeutic Fab Epratuzumab
Components
  • (Epratuzumab Fab ...) x 2
  • B-cell receptor CD22
KeywordsIMMUNE SYSTEM / therapeutic antibody / Siglec / B cell / Fab
Function / homologyImmunoglobulin domain / Immunoglobulin-like fold / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / CD22 mediated BCR regulation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Ig-like domain profile. / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin domain / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain ...Immunoglobulin domain / Immunoglobulin-like fold / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / CD22 mediated BCR regulation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Ig-like domain profile. / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin domain / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin C1-set domain / Immunoglobulin-like domain superfamily / CD80-like, immunoglobulin C2-set / Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin subtype 2 / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / carbohydrate binding / cell adhesion / extracellular exosome / integral component of membrane / plasma membrane / B-cell receptor CD22 / Uncharacterized protein / IgG H chain
Function and homology information
Specimen sourceHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.1 Å resolution
AuthorsSicard, T. / Ereno-Orbea, J. / Julien, J.P.
CitationJournal: Nat Commun / Year: 2017
Title: Molecular basis of human CD22 function and therapeutic targeting.
Authors: June Ereño-Orbea / Taylor Sicard / Hong Cui / Mohammad T Mazhab-Jafari / Samir Benlekbir / Alba Guarné / John L Rubinstein / Jean-Philippe Julien
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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Protein/peptide , 1 types, 4 molecules QRST

#1: Protein/peptide
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 (human) / Gene: CD22, SIGLEC2 / Production host: Homo sapiens (human) / References: UniProt: P20273

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

#2: Protein/peptide
Epratuzumab Fab Heavy Chain


Mass: 24028.684 Da / Num. of mol.: 4
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens (human) / References: UniProt: S6B291
#3: Protein/peptide
Epratuzumab Fab Light Chain


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

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Non-polymers , 4 types, 25 molecules

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


Mass: 221.208 Da / Num. of mol.: 16 / Formula: C8H15NO6 / N-Acetylglucosamine
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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

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Experimental details

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Experiment

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

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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

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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

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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

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