[English] 日本語
Yorodumi
- PDB-5g64: The complex between human IgE-Fc and two anti-IgE Fab fragments -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g64
TitleThe complex between human IgE-Fc and two anti-IgE Fab fragments
Components
  • (FAB FRAGMENTFragment antigen-binding) x 2
  • IG EPSILON CHAIN C REGION
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN E / OMALIZUMAB / IGE-FC
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.715 Å
AuthorsDavies, A.M. / Allan, E.G. / Keeble, A.H. / Delgado, J. / Cossins, B.P. / Mitropoulou, A.N. / Pang, M.O.Y. / Ceska, T. / Beavil, A.J. / Craggs, G. ...Davies, A.M. / Allan, E.G. / Keeble, A.H. / Delgado, J. / Cossins, B.P. / Mitropoulou, A.N. / Pang, M.O.Y. / Ceska, T. / Beavil, A.J. / Craggs, G. / Westwood, M. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab.
Authors: Davies, A.M. / Allan, E.G. / Keeble, A.H. / Delgado, J. / Cossins, B.P. / Mitropoulou, A.N. / Pang, M.O.Y. / Ceska, T. / Beavil, A.J. / Craggs, G. / Westwood, M. / Henry, A.J. / McDonnell, J.M. / Sutton, B.J.
History
DepositionJun 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IG EPSILON CHAIN C REGION
B: IG EPSILON CHAIN C REGION
H: FAB FRAGMENT
I: FAB FRAGMENT
L: FAB FRAGMENT
M: FAB FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8878
Polymers170,0656
Non-polymers1,8222
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint5.9 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.640, 231.190, 247.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

-
Components

#1: Protein IG EPSILON CHAIN C REGION / IMMUNOGLOBULIN E


Mass: 36354.781 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN E-FC / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): MOUSE MYELOMA NS0 / Production host: MUS MUSCULUS (house mouse)
#2: Antibody FAB FRAGMENT / Fragment antigen-binding


Mass: 24672.490 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN, RESIDUES 1-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK / Production host: HOMO SAPIENS (human)
#3: Antibody FAB FRAGMENT / Fragment antigen-binding


Mass: 24005.426 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN, RESIDUES 1-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK / Production host: HOMO SAPIENS (human)
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
Sequence detailsRESIDUES 222-223 ARE FROM THE EXPRESSION VECTOR. RESIDUE 225 - DISULPHIDE BOND MUTANT. RESIDUES 265 ...RESIDUES 222-223 ARE FROM THE EXPRESSION VECTOR. RESIDUE 225 - DISULPHIDE BOND MUTANT. RESIDUES 265 AND 371 - MUTATIONS TO REMOVE GLYCOSYLATION SITES.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 62 %
Description: SCALED DATA WERE TRUNCATED USING THE UCLA DIFFRACTION ANISOTROPY SERVER, AND THEN USED FOR REFINEMENT. SEE ASSOCIATED PUBLICATION FOR FURTHER DETAILS
Crystal growDetails: 4% PEG 8000 AND 0.03M SODIUM FLUORIDE. CRYSTALS WERE CRYOPROTECTED WITH 4M TMAO

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0210.976
SYNCHROTRONDiamond I0320.976
Detector
TypeIDDetectorDate
PILATUS1PIXELFeb 11, 2012
PILATUS2PIXEL
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.7→115.59 Å / Num. obs: 23989 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 38 % / Biso Wilson estimate: 115.86 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 17.9
Reflection shellResolution: 3.7→4 Å / Redundancy: 38.4 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

-
Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2WQR AND UNPUBLISHED FAB STRUCTURE

2wqr


Resolution: 3.715→115.595 Å / SU ML: 0.6 / σ(F): 1.36 / Phase error: 35.44 / Stereochemistry target values: ML
Details: DATA USED FOR REFINEMENT WERE TRUNCATED USING THE UCLA DIFFRACTION ANISOTROPY SERVER
RfactorNum. reflection% reflection
Rfree0.3092 1007 5 %
Rwork0.2588 --
obs0.2614 20087 84.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.715→115.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10783 0 122 0 10905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211202
X-RAY DIFFRACTIONf_angle_d0.45115366
X-RAY DIFFRACTIONf_dihedral_angle_d9.1276607
X-RAY DIFFRACTIONf_chiral_restr0.0391794
X-RAY DIFFRACTIONf_plane_restr0.0041957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.715-3.91090.35430.34564X-RAY DIFFRACTION20
3.91-4.15590.369120.326223X-RAY DIFFRACTION70
4.155-4.47680.367160.296319X-RAY DIFFRACTION90
4.476-4.92730.348160.271317X-RAY DIFFRACTION100
4.927-5.64030.325160.27321X-RAY DIFFRACTION100
5.64-7.10610.344170.299324X-RAY DIFFRACTION100
7.106-115.65090.244180.206338X-RAY DIFFRACTION100
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)
10.1158-0.02070.10180.0196-0.01040.09060.16540.11670.1078-0.1463-0.1477-0.05510.33420.20650.07621.24460.0364-0.02291.09940.67661.2995-7.30874.9458-86.9411
20.02840.0342-0.06330.0337-0.07010.14020.1312-0.1539-0.06860.1559-0.05790.0033-0.19270.15380.2470.7448-0.12190.0281.26490.78651.425414.33121.9988-50.1978
30.04340.0148-0.01480.01490.00790.0098-0.0645-0.07030.26580.11180.0058-0.3447-0.12690.059901.706-0.79190.02432.19420.01762.0144-0.415240.65-30.7424
40.01130.00880.00980.02440.01410.01050.023-0.01120.0518-0.0368-0.0429-0.0279-0.0030.09480.1041.0803-0.34320.06160.96980.69511.445-11.57221.7513-77.0484
50.05030.0216-0.02930.0123-0.01750.06020.09260.2280.20380.0669-0.03770.1272-0.1718-0.0523-0.18180.872-0.3460.120.94240.47611.1573-32.917919.7419-46.3073
60.0287-0.016-0.01120.01590.00960.01730.0849-0.29040.2332-0.0692-0.17040.0974-0.0577-0.0659-01.642-0.339-0.06581.2831-0.03972.4069-18.136143.329-35.1747
70.05280.0391-0.10340.06510.0020.39710.0782-0.2275-0.15350.01940.0105-0.0921-0.04720.07740.19970.1383-0.1930.19770.50860.67991.192133.56237.7337-72.4552
80.02870.03310.02630.04820.00480.070.02350.1131-0.07820.0378-0.08440.0343-0.0781-0.11640.15830.1108-0.3069-0.01810.3901-0.3696-0.085620.765259.147-92.621
90.0411-0.0045-0.02250.00620.00310.0324-0.17770.03390.0223-0.09290.0970.07670.2774-0.0966-0.15191.5322-0.13450.77550.81890.18411.5245-52.71734.1697-24.0048
100.0169-0.0133-0.01070.0307-0.01840.0215-0.0159-0.13250.0455-0.0670.1012-0.0938-0.0023-0.05620.04911.68870.18010.71641.8936-0.19631.1246-42.6763-14.8937-0.6
110.04360.0657-0.03160.1204-0.03930.0193-0.1746-0.0229-0.2078-0.0648-0.0773-0.13450.25990.0069-0.61430.3541-0.15380.265-0.11670.32041.152914.738327.1357-78.5241
120.00770.01040.00820.0436-0.00120.037-0.1566-0.0995-0.1852-0.120.09830.04430.2236-0.0782-0.191.81170.04460.75431.09770.39121.3155-36.3467-5.8353-35.2414
130.1440.04260.11640.01980.01760.1029-0.03320.4532-0.1267-0.18940.1976-0.07640.20510.07220.29150.6512-0.5637-0.07631.5271-0.40060.038714.150953.0896-105.8464
140.10020.04160.05680.01780.01960.03930.0867-0.14050.0059-0.1229-0.2006-0.08330.0918-0.1041-0.13032.34060.23670.83521.3010.2941.1189-38.1156-30.6807-6.4015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 229:329
2X-RAY DIFFRACTION2CHAIN A AND RESID 333:440
3X-RAY DIFFRACTION3CHAIN A AND RESID 441:543
4X-RAY DIFFRACTION4CHAIN B AND RESID 230:328
5X-RAY DIFFRACTION5CHAIN B AND RESID 332:440
6X-RAY DIFFRACTION6CHAIN B AND RESID 441:543
7X-RAY DIFFRACTION7CHAIN H AND RESID 1:121
8X-RAY DIFFRACTION8CHAIN H AND RESID 122:230
9X-RAY DIFFRACTION9CHAIN I AND RESID 1:121
10X-RAY DIFFRACTION10CHAIN I AND RESID 122:230
11X-RAY DIFFRACTION11CHAIN L AND RESID 1:111
12X-RAY DIFFRACTION12CHAIN M AND RESID 1:111
13X-RAY DIFFRACTION13CHAIN L AND RESID 112:230
14X-RAY DIFFRACTION14CHAIN M AND RESID 112:230

+
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