[English] 日本語
Yorodumi
- PDB-7re9: TCR mimic antibody (Fab fragment) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7re9
TitleTCR mimic antibody (Fab fragment)
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / TCR mimic antibody (Fab fragment)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsDasgupta, M. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Rep / Year: 2022
Title: Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma.
Authors: Liu, C. / Liu, H. / Dasgupta, M. / Hellman, L.M. / Zhang, X. / Qu, K. / Xue, H. / Wang, Y. / Fan, F. / Chang, Q. / Yu, D. / Ge, L. / Zhang, Y. / Cui, Z. / Zhang, P. / Heller, B. / Zhang, H. ...Authors: Liu, C. / Liu, H. / Dasgupta, M. / Hellman, L.M. / Zhang, X. / Qu, K. / Xue, H. / Wang, Y. / Fan, F. / Chang, Q. / Yu, D. / Ge, L. / Zhang, Y. / Cui, Z. / Zhang, P. / Heller, B. / Zhang, H. / Shi, B. / Baker, B.M. / Liu, C.
History
DepositionJul 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
A: Fab heavy chain
B: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1056
Polymers93,8924
Non-polymers2122
Water97354
1
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1584
Polymers46,9462
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-19 kcal/mol
Surface area18960 Å2
MethodPISA
2
A: Fab heavy chain
B: Fab light chain


Theoretical massNumber of molelcules
Total (without water)46,9462
Polymers46,9462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-20 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.325, 40.348, 161.807
Angle α, β, γ (deg.)90.000, 105.150, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 131 or resid 139 through 217))
21(chain H and (resid 2 through 131 or resid 139 through 217))
12(chain B and resid 3 through 212)
22(chain L and resid 3 through 212)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALSERSER(chain A and (resid 2 through 131 or resid 139 through 217))AC2 - 1312 - 131
121THRTHRPROPRO(chain A and (resid 2 through 131 or resid 139 through 217))AC139 - 217139 - 217
211VALVALSERSER(chain H and (resid 2 through 131 or resid 139 through 217))HA2 - 1312 - 131
221THRTHRPROPRO(chain H and (resid 2 through 131 or resid 139 through 217))HA139 - 217139 - 217
112VALVALPROPRO(chain B and resid 3 through 212)BD3 - 2123 - 212
212VALVALPROPRO(chain L and resid 3 through 212)LB3 - 2123 - 212

NCS ensembles :
ID
1
2

-
Components

#1: Antibody Fab heavy chain


Mass: 24068.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab light chain


Mass: 22877.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 15% w/v Polyethylene glycol 6,000 and 5.00 % w/v Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.77→66.35 Å / Num. obs: 21759 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.967 / Net I/σ(I): 8.9
Reflection shellResolution: 2.77→2.82 Å / Num. unique obs: 1118 / CC1/2: 0.516

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHENIXmodel building
DIALSdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M6M, 6PZH

4m6m

6pzh


Resolution: 2.77→66.33 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 2147 9.99 %
Rwork0.2231 19336 -
obs0.2275 21483 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.25 Å2 / Biso mean: 33.3405 Å2 / Biso min: 0.99 Å2
Refinement stepCycle: final / Resolution: 2.77→66.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 0 14 54 6377
Biso mean--46.75 11.79 -
Num. residues----840
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1849X-RAY DIFFRACTION9.685TORSIONAL
12H1849X-RAY DIFFRACTION9.685TORSIONAL
21B1881X-RAY DIFFRACTION9.685TORSIONAL
22L1881X-RAY DIFFRACTION9.685TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.77-2.830.42281440.31291278142297
2.83-2.910.37141360.29461250138695
2.91-2.980.33171380.28781222136097
2.98-3.070.31341420.2861286142896
3.07-3.170.32081380.26361256139498
3.17-3.280.31041410.26641260140197
3.28-3.420.33621430.26341276141998
3.42-3.570.25661380.22811268140697
3.57-3.760.29461460.22381308145499
3.76-3.990.25121440.19211297144199
4-4.30.20781470.187313211468100
4.3-4.740.16881450.15581298144399
4.74-5.420.18451450.1581314145999
5.42-6.830.26121470.21111322146997
6.83-66.330.27241530.22231380153398
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)
12.865-1.3844-1.14993.58521.04642.57050.02280.64270.4793-0.6325-0.58170.4173-0.7057-0.6443-0.6230.24040.0735-0.05080.1449-0.0730.31010.43815.08857.5875
22.44490.8217-0.76752.39290.09682.39240.0836-0.1545-0.0075-0.0656-0.04490.04440.26950.0367-0.03670.199-0.0161-0.03340.1891-0.0360.182818.869-5.618247.7261
36.2651.38180.37951.2702-0.54671.45840.2213-0.5191-1.39320.3476-0.1891-0.76110.4914-0.3612-0.11620.3635-0.11190.02240.245-0.02750.274620.8382-14.302853.0834
41.6268-1.40390.12831.5841-0.40631.32140.1279-0.1190.0608-0.0627-0.02210.0010.0038-0.0043-0.03440.2292-0.0236-0.00740.2005-0.02110.216851.5094-5.797546.8441
53.2578-0.21722.03012.534-1.11492.72330.039-0.17840.10470.0434-0.05810.19720.4809-0.26260.0760.2531-0.10220.01130.3333-0.0350.225923.0884-15.46369.0355
63.20691.4718-1.57062.7334-2.24612.714-0.0001-0.04070.14330.2226-0.02790.0799-0.25540.0670.05230.2537-0.0463-0.0010.2568-0.00850.180358.1145-2.053362.0681
72.2951-1.59620.66171.1154-0.48170.5064-0.00410.0037-0.0088-0.03880.16330.41810.36350.58540.12770.37270.07790.04280.1359-0.02810.306833.0838-11.037732.1222
80.30280.38970.02072.03030.26771.5679-0.1324-0.0089-0.17760.41830.11680.0447-0.14050.12890.03590.27260.00820.01980.12690.04660.282439.772-13.408328.1439
92.83311.15180.95251.2051-1.51245.48960.12430.5118-0.7166-0.2937-0.234-0.33350.18060.7842-0.34350.2936-0.0267-0.06840.2229-0.0590.273148.4518-16.246524.6009
101.99330.0334-0.40494.749-1.02914.46610.31930.3750.0956-0.61610.1711-0.57160.02260.86280.71550.1778-0.0744-0.11310.2060.1420.175147.3502-11.384628.5905
111.44320.51960.18692.6899-0.50771.76520.08780.328-0.1424-0.2061-0.1795-0.1592-0.08480.17680.09090.15950.0097-0.00280.143-0.02450.243138.6714-11.853625.5765
120.6248-0.5042-1.81862.70641.39445.50380.3033-0.34040.79380.198-0.77210.44740.1126-1.3818-0.79540.4497-0.1489-0.0537-0.28870.09040.2411.87385.245326.6089
131.56640.4526-0.28141.19160.10991.9426-0.2599-0.0743-0.0044-0.50450.1167-0.07050.2804-0.3301-0.01370.22350.0188-0.04630.217-0.01370.37213.4208-1.007424.9919
142.7173-2.6661-0.03262.65670.2312.4979-1.0285-0.3301-0.7365-0.25960.08460.75640.2491-1.0461-0.18880.3593-0.1096-0.00490.5385-0.15520.3186-1.1048-6.304628.4261
152.13251.38381.01520.88250.70732.30070.3707-0.2361-0.62940.1091-0.0171-0.49050.3766-0.39010.37460.1395-0.0216-0.0090.2805-0.00120.324716.2931-0.632333.6057
164.05381.12070.31693.0712-0.58750.30240.4259-0.54760.54750.0136-0.50410.6126-0.25020.19510.05410.40540.10070.09930.4183-0.10730.29857.63571.7334.9635
172.08410.05470.70432.9251-0.14893.6918-0.15910.3761-0.0806-0.0980.1902-0.1092-0.14640.3842-0.07850.2509-0.06230.03330.2384-0.10850.281434.5036-23.87628.922
182.33440.1048-0.75721.0081-0.42060.9365-0.1312-0.28150.1280.07350.18460.2792-0.2468-0.0608-0.00540.49770.114-0.05430.2421-0.03580.35434.94041.654916.5478
192.84110.6877-0.24662.39221.07263.7854-0.0562-0.0790.17740.0550.1702-0.0631-0.04350.12510.01690.19360.0511-0.0420.25230.00910.268.49493.580211.688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 192 through 212 )L192 - 212
2X-RAY DIFFRACTION2chain 'A' and (resid 2 through 91 )A2 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 110 )A92 - 110
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 217 )A111 - 217
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 109 )B3 - 109
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 213 )B110 - 213
7X-RAY DIFFRACTION7chain 'H' and (resid 2 through 12 )H2 - 12
8X-RAY DIFFRACTION8chain 'H' and (resid 13 through 44 )H13 - 44
9X-RAY DIFFRACTION9chain 'H' and (resid 45 through 60 )H45 - 60
10X-RAY DIFFRACTION10chain 'H' and (resid 61 through 77 )H61 - 77
11X-RAY DIFFRACTION11chain 'H' and (resid 78 through 115 )H78 - 115
12X-RAY DIFFRACTION12chain 'H' and (resid 116 through 139 )H116 - 139
13X-RAY DIFFRACTION13chain 'H' and (resid 140 through 181 )H140 - 181
14X-RAY DIFFRACTION14chain 'H' and (resid 182 through 198 )H182 - 198
15X-RAY DIFFRACTION15chain 'H' and (resid 199 through 207 )H199 - 207
16X-RAY DIFFRACTION16chain 'H' and (resid 208 through 217 )H208 - 217
17X-RAY DIFFRACTION17chain 'L' and (resid 3 through 109 )L3 - 109
18X-RAY DIFFRACTION18chain 'L' and (resid 110 through 133 )L110 - 133
19X-RAY DIFFRACTION19chain 'L' and (resid 134 through 191 )L134 - 191

+
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