[English] 日本語
Yorodumi
- PDB-5vkk: Crystal structure of Fab fragment of anti-CD22 Epratuzumab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vkk
TitleCrystal structure of Fab fragment of anti-CD22 Epratuzumab
Components
  • Epratuzumab Fab Heavy Chain
  • Epratuzumab Fab Light Chain
KeywordsIMMUNE SYSTEM / therapeutic antibody / B cell
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.014 Å
AuthorsSicard, T. / Ereno-Orbea, J. / Julien, J.P.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)111111 Canada
Canadian Institutes of Health Research (CIHR)PJT-148811 Canada
Canadian Institutes of Health Research (CIHR)BPF-144483 Canada
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 /
Abstract: CD22 maintains a baseline level of B-cell inhibition to keep humoral immunity in check. As a B-cell-restricted antigen, CD22 is targeted in therapies against dysregulated B cells that cause ...CD22 maintains a baseline level of B-cell inhibition to keep humoral immunity in check. As a B-cell-restricted antigen, CD22 is targeted in therapies against dysregulated B cells that cause autoimmune diseases and blood cancers. Here we report the crystal structure of human CD22 at 2.1 Å resolution, which reveals that specificity for α2-6 sialic acid ligands is dictated by a pre-formed β-hairpin as a unique mode of recognition across sialic acid-binding immunoglobulin-type lectins. The CD22 ectodomain adopts an extended conformation that facilitates concomitant CD22 nanocluster formation on B cells and binding to trans ligands to avert autoimmunity in mammals. We structurally delineate the CD22 site targeted by the therapeutic antibody epratuzumab at 3.1 Å resolution and determine a critical role for CD22 N-linked glycosylation in antibody engagement. Our studies provide molecular insights into mechanisms governing B-cell inhibition and valuable clues for the design of immune modulators in B-cell dysfunction.The B-cell-specific co-receptor CD22 is a therapeutic target for depleting dysregulated B cells. Here the authors structurally characterize the ectodomain of CD22 and present its crystal structure with the bound therapeutic antibody epratuzumab, which gives insights into the mechanism of inhibition of B-cell activation.
History
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.2Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Epratuzumab Fab Heavy Chain
L: Epratuzumab Fab Light Chain
A: Epratuzumab Fab Heavy Chain
B: Epratuzumab Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)95,5904
Polymers95,5904
Non-polymers00
Water9,062503
1
H: Epratuzumab Fab Heavy Chain
L: Epratuzumab Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,7952
Polymers47,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-29 kcal/mol
Surface area19600 Å2
MethodPISA
2
A: Epratuzumab Fab Heavy Chain
B: Epratuzumab Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)47,7952
Polymers47,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-27 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.712, 61.564, 65.285
Angle α, β, γ (deg.)71.81, 81.07, 75.95
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody Epratuzumab Fab Heavy Chain


Mass: 23741.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: DKFZp686P15220 / Production host: Homo sapiens (human) / References: UniProt: Q6N089
#2: Antibody Epratuzumab Fab Light Chain


Mass: 24053.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 85 mM Tris, pH 8.5, 25.5% PEG 4000 (w/v), 170 mM sodium acetate and 15% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.014→49.671 Å / Num. obs: 52026 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 2.957 % / CC1/2: 0.993 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.177 / Χ2: 0.963 / Net I/σ(I): 6.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.014-2.082.9790.7561.7151190.6260.92896
2.08-2.162.980.5982.1849350.670.73196.7
2.16-2.252.9880.5072.747740.7430.61996.9
2.25-2.352.9860.4243.2446280.8210.51696.8
2.35-2.462.9910.3493.9244000.860.42597
2.46-2.592.9910.2615.1341890.9140.31897.1
2.59-2.752.9840.1986.6739510.9480.2497.3
2.75-2.942.9820.1349.1637250.9750.16397.4
2.94-3.182.9920.09312.734430.9880.11297.2
3.18-3.482.9580.06516.6931930.9930.0896.9
3.48-3.892.9590.04820.9528700.9950.05996.8
3.89-4.492.9560.03825.125110.9960.04696.4
4.49-5.52.9260.03326.4621380.9970.0496.8
5.5-7.782.9220.03624.5516720.9970.04597.2
7.78-49.6712.9070.02830.199080.9980.03597.5

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANI

6ani


Resolution: 2.014→49.671 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 2000 3.84 %
Rwork0.2121 --
obs0.2131 52020 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.014→49.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6681 0 0 503 7184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046853
X-RAY DIFFRACTIONf_angle_d0.8339329
X-RAY DIFFRACTIONf_dihedral_angle_d14.794095
X-RAY DIFFRACTIONf_chiral_restr0.0521044
X-RAY DIFFRACTIONf_plane_restr0.0051181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0144-2.06470.33381380.31773449X-RAY DIFFRACTION93
2.0647-2.12060.35911410.29693526X-RAY DIFFRACTION96
2.1206-2.1830.27081430.27683595X-RAY DIFFRACTION97
2.183-2.25340.25951430.26813563X-RAY DIFFRACTION97
2.2534-2.3340.3151440.2643591X-RAY DIFFRACTION97
2.334-2.42740.30421430.2553571X-RAY DIFFRACTION97
2.4274-2.53790.30861420.25193564X-RAY DIFFRACTION98
2.5379-2.67170.27791450.24553624X-RAY DIFFRACTION98
2.6717-2.83910.27571450.23223626X-RAY DIFFRACTION98
2.8391-3.05820.24941420.21493563X-RAY DIFFRACTION98
3.0582-3.36590.2241440.20073597X-RAY DIFFRACTION98
3.3659-3.85280.20271440.18173595X-RAY DIFFRACTION97
3.8528-4.85350.18041430.15683560X-RAY DIFFRACTION97
4.8535-49.68630.18121430.18453595X-RAY DIFFRACTION98
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)
11.5602-0.7757-0.38292.2738-0.82961.5394-0.0518-0.00750.5132-0.1622-0.0894-0.07140.02610.0357-0.06190.1801-0.04290.05640.24760.02290.180631.845852.380719.1016
21.3301-0.64010.52022.8059-0.1170.78250.00880.0579-0.0878-0.0437-0.04750.2730.02980.01270.04890.1884-0.05060.01630.24740.0130.249218.75253.726919.766
32.0754-1.31730.37014.0244-0.97421.0908-0.2658-0.6370.30210.33620.24860.2373-0.0758-0.40020.00110.23140.00350.04760.2655-0.05770.281319.316958.812329.2534
41.1433-0.3612-0.1512.05410.1790.8557-0.0689-0.08440.05920.22460.0483-0.00860.05780.16780.03050.2082-0.0188-0.00250.2318-0.02010.196128.184154.8123.4021
50.87140.6426-0.93661.78830.62281.54420.07460.20730.3425-0.3501-0.14650.3575-0.0645-0.19580.06910.1778-0.0113-0.02210.1540.03990.229717.699450.945413.6573
60.4038-0.5235-0.54391.5913-0.38860.70850.06240.0587-0.1576-0.1722-0.17450.37880.1050.02860.09140.15370.0132-0.04150.2005-0.02080.251341.344125.016715.8464
71.10240.80410.44881.40380.9072.0146-0.01280.1628-0.03-0.1775-0.10690.26290.09450.00550.07220.15410.0129-0.00980.2713-0.00490.190645.965426.56597.9684
81.20990.5262-0.19993.56430.31691.5932-0.0392-0.0624-0.2596-0.20580.0282-0.92560.15480.30560.11810.19450.06510.00480.28840.00270.256750.298622.55911.4371
91.65770.1232-0.66621.88930.5411.11750.0782-0.13810.22040.1097-0.04520.2761-0.0805-0.0710.0250.1986-0.05280.03770.2650.01230.28414.879839.804220.3204
101.1296-0.28340.26360.68750.00780.43020.00940.06560.0449-0.0528-0.0280.1122-0.0033-0.02640.0290.1896-0.05220.04880.24420.01880.199917.726232.502416.2571
112.966-0.00590.70881.59660.46590.9234-0.1691-0.11990.01390.07990.1682-0.04990.0401-0.04590.01010.23020.00420.01320.21060.01630.244830.970618.27923.4568
122.2569-0.24640.67130.72450.32860.51080.0051-0.2651-0.37960.40360.1943-0.16990.2639-0.0515-0.20120.3010.0321-0.07290.33020.07740.368241.279710.779228.4954
133.21140.2029-0.71022.8458-0.11242.74350.1542-0.1076-0.18030.0269-0.22060.34340.32210.134-0.08650.26460.0095-0.04210.18630.01210.1872.950117.423343.9654
142.0665-0.26560.23252.67740.41382.00330.1055-0.09010.00270.0840.0575-0.0498-0.0988-0.1523-0.16920.28320.0562-0.05230.2876-0.0230.18236.438629.917748.2776
151.11710.32740.78822.2090.11971.10890.0508-0.0452-0.02370.03510.020.12740.0245-0.1323-0.01770.23520.0467-0.01360.2-0.00680.17793.671227.683244.7202
160.6919-0.4194-0.24551.78120.70390.20370.21130.1653-0.0708-0.2188-0.36890.26450.17220.18320.17140.36690.1194-0.06260.3147-0.02410.251323.3391-2.547548.1397
171.83760.17890.67732.33371.44291.9056-0.0073-0.28180.0364-0.0942-0.31110.5718-0.0396-0.44810.14730.35860.00510.01670.3964-0.05720.320920.757-2.772454.1944
180.7149-0.28180.21491.62190.32770.7350.02090.10490.0819-0.29210.0417-0.1864-0.21810.1147-0.04440.3388-0.0408-0.01430.2224-0.00630.262822.445931.75357.9131
191.0604-1.43930.31852.24731.76451.65930.37320.23140.3377-0.548-0.0023-0.7974-0.22260.2264-0.20330.45580.06830.12910.3393-0.02740.44736.2976-1.172148.0174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 23 )
2X-RAY DIFFRACTION2chain 'H' and (resid 24 through 52 )
3X-RAY DIFFRACTION3chain 'H' and (resid 53 through 67 )
4X-RAY DIFFRACTION4chain 'H' and (resid 68 through 91 )
5X-RAY DIFFRACTION5chain 'H' and (resid 92 through 109 )
6X-RAY DIFFRACTION6chain 'H' and (resid 110 through 191 )
7X-RAY DIFFRACTION7chain 'H' and (resid 192 through 203 )
8X-RAY DIFFRACTION8chain 'H' and (resid 204 through 219 )
9X-RAY DIFFRACTION9chain 'L' and (resid 1 through 38 )
10X-RAY DIFFRACTION10chain 'L' and (resid 39 through 133 )
11X-RAY DIFFRACTION11chain 'L' and (resid 134 through 179 )
12X-RAY DIFFRACTION12chain 'L' and (resid 180 through 219 )
13X-RAY DIFFRACTION13chain 'A' and (resid 3 through 24 )
14X-RAY DIFFRACTION14chain 'A' and (resid 25 through 51 )
15X-RAY DIFFRACTION15chain 'A' and (resid 52 through 109 )
16X-RAY DIFFRACTION16chain 'A' and (resid 110 through 148 )
17X-RAY DIFFRACTION17chain 'A' and (resid 149 through 219 )
18X-RAY DIFFRACTION18chain 'B' and (resid 1 through 118 )
19X-RAY DIFFRACTION19chain 'B' and (resid 119 through 219 )

+
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