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- PDB-7k0z: Marsupial T cell receptor Spl_157 -

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Basic information

Entry
Database: PDB / ID: 7k0z
TitleMarsupial T cell receptor Spl_157
Components
  • T cell receptor gamma chain
  • T cell receptor mu chain
KeywordsIMMUNE SYSTEM / T cell receptor / antigen recognition / IgV domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMonodelphis domestica (gray short-tailed opossum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWegrecki, M. / Kannan Sivaraman, K. / Le Nours, J. / Rossjohn, J.
CitationJournal: Science / Year: 2021
Title: The molecular assembly of the marsupial gamma mu T cell receptor defines a third T cell lineage.
Authors: Morrissey, K.A. / Wegrecki, M. / Praveena, T. / Hansen, V.L. / Bu, L. / Sivaraman, K.K. / Darko, S. / Douek, D.C. / Rossjohn, J. / Miller, R.D. / Le Nours, J.
History
DepositionSep 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: T cell receptor mu chain
D: T cell receptor gamma chain
A: T cell receptor mu chain
B: T cell receptor gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,6385
Polymers130,4174
Non-polymers2211
Water00
1
C: T cell receptor mu chain
D: T cell receptor gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4303
Polymers65,2082
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-19 kcal/mol
Surface area25950 Å2
MethodPISA
2
A: T cell receptor mu chain
B: T cell receptor gamma chain


Theoretical massNumber of molelcules
Total (without water)65,2082
Polymers65,2082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-26 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.328, 110.722, 207.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

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
111ALAALATHRTHR(chain 'D' and (resid 6 through 11 or (resid 12...DB6 - 256 - 25
121VALVALSERSER(chain 'D' and (resid 6 through 11 or (resid 12...DB28 - 3328 - 33
131ILEILELYSLYS(chain 'D' and (resid 6 through 11 or (resid 12...DB36 - 7536 - 75
141PHEPHEASNASN(chain 'D' and (resid 6 through 11 or (resid 12...DB78 - 7978 - 79
151LYSLYSTRPTRP(chain 'D' and (resid 6 through 11 or (resid 12...DB82 - 10382 - 103
161ASPASPLYSLYS(chain 'D' and (resid 6 through 11 or (resid 12...DB106 - 167106 - 167
171ASNASNVALVAL(chain 'D' and (resid 6 through 11 or (resid 12...DB171 - 197171 - 197
181ASNASNPHEPHE(chain 'D' and (resid 6 through 11 or (resid 12...DB205 - 222205 - 222
211ALAALATHRTHR(chain 'B' and (resid 6 through 26 or resid 28...BD6 - 256 - 25
221VALVALSERSER(chain 'B' and (resid 6 through 26 or resid 28...BD28 - 3328 - 33
231ILEILELYSLYS(chain 'B' and (resid 6 through 26 or resid 28...BD36 - 7536 - 75
241PHEPHEASNASN(chain 'B' and (resid 6 through 26 or resid 28...BD78 - 7978 - 79
251LYSLYSTRPTRP(chain 'B' and (resid 6 through 26 or resid 28...BD82 - 10382 - 103
261ASPASPLYSLYS(chain 'B' and (resid 6 through 26 or resid 28...BD106 - 167106 - 167
271ASNASNVALVAL(chain 'B' and (resid 6 through 26 or resid 28...BD171 - 197171 - 197
281ASNASNPHEPHE(chain 'B' and (resid 6 through 26 or resid 28...BD205 - 222205 - 222
112LEULEUCYSCYS(chain 'A' and ((resid 11 and (name N or name...AC11 - 10411 - 104
122LEULEUPROPRO(chain 'A' and ((resid 11 and (name N or name...AC120 - 137120 - 137
212LEULEUCYSCYS(chain 'C' and (resid 11 through 135 or (resid 136...CA11 - 10411 - 104
222LEULEUPROPRO(chain 'C' and (resid 11 through 135 or (resid 136...CA120 - 137120 - 137

NCS ensembles :
ID
1
2

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Components

#1: Protein T cell receptor mu chain


Mass: 38203.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monodelphis domestica (gray short-tailed opossum)
Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#2: Protein T cell receptor gamma chain


Mass: 27004.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monodelphis domestica (gray short-tailed opossum)
Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M CBTP pH 8.8, 15-20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→47.03 Å / Num. obs: 28367 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 87.45 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 3.2→3.39 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4496 / Rpim(I) all: 0.545

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished

Resolution: 3.2→47.03 Å / SU ML: 0.5363 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.866
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2855 1121 3.96 %
Rwork0.2573 27167 -
obs0.2585 28288 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.45 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7922 0 14 0 7936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00338126
X-RAY DIFFRACTIONf_angle_d0.80611090
X-RAY DIFFRACTIONf_chiral_restr0.0481256
X-RAY DIFFRACTIONf_plane_restr0.00511438
X-RAY DIFFRACTIONf_dihedral_angle_d16.21711147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.350.41881400.37783316X-RAY DIFFRACTION99.91
3.35-3.520.38971300.31753353X-RAY DIFFRACTION99.86
3.52-3.740.34471400.29963346X-RAY DIFFRACTION99.91
3.74-4.030.30291300.26093375X-RAY DIFFRACTION100
4.03-4.440.28671400.23573372X-RAY DIFFRACTION99.89
4.44-5.080.22911490.2163391X-RAY DIFFRACTION99.94
5.08-6.390.27661310.2533425X-RAY DIFFRACTION99.97
6.4-47.030.25591610.24323589X-RAY DIFFRACTION99.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.581497559570.805152758015-1.745384994474.65805186093-2.316326120114.63911984873-0.701008415361-0.9199183171180.125189457497-0.79847100312-0.360234323171-1.567719630320.113947253190.3127075351040.7175737868270.6882482179250.03961241626260.1099236479081.1246828598-0.1189931932951.6181627318810.70645711350.424217141004-87.3593226977
25.46582620277-0.481215824337-0.09971047181242.94478645877-0.9582317121946.60611029653-0.593233583245-0.7033500263890.009740693830840.5062767609650.73768901477-0.04434797911540.7763964356291.115927596170.004908926745970.8322250899910.2764951394450.003797129368470.7784620267570.05981102507130.670781131306-8.32314617918-7.33380225207-50.7078146768
32.686645829490.509541060134-1.229703896691.90452918734-1.011868530251.60414789939-0.852509755696-1.6616542829-0.1356465696950.9303688769230.8783072577790.8902792436620.7736334862450.107185525717-0.103558410131.046843860820.3166332529540.4155830604471.470789068360.3799516019470.962625290896-39.37498693044.2075377442-32.1633775939
44.79182255498-1.47125609677-1.839686056485.91598712782-0.9614823944681.14441299130.600030875817-1.074208385480.4986882813541.416663056430.481961964343-0.0807322712147-1.73729312261-0.289391802513-0.2979065924210.7422870660680.4352561832450.2227093037021.879246562320.07589880891380.530205341211-17.842075793916.2227325488-52.5964687577
57.24440228175-1.91436770254-2.141461596064.043023448050.2058869554.178650205790.245871042858-1.084104209150.769926474890.561068919680.5347190182340.327599534385-0.7319203504080.342764369621-0.5607125208210.575065712358-0.07827097383240.1389565334690.8922329567620.08869683541340.436401394809-12.814150009814.4682099087-58.9214114569
66.406390482721.72573724116-0.7731017804525.70882321029-1.488341825045.375171889030.333943238639-1.30667462592-0.5649271646810.0452857692309-0.2051789431260.658497572207-0.628652681363-0.475349409042-0.2361298293880.592196501730.01513913685650.01189075026150.483088855850.1447115200220.527814466773-15.21477178414.7551880507-62.0191773973
78.246952407391.16076507347-0.6828061597484.56885556268-0.2683404528875.87069603276-0.3812587609570.2350919735870.7527479335470.7712663668820.04120366736530.237048101601-0.8371890203440.163451600537-0.2697965890420.803340634033-0.0008461562819270.04401134797780.6378122489580.1070538663540.531716828293-8.849764339611.3358824183-68.4849096295
83.37525461634-1.90158953881-1.81950512032.69867426383-1.64329988036.136478973880.3571995358660.4101457956690.6902561657920.09418236245450.04435590771550.238878555605-1.06973132038-0.941182873358-0.391606628550.773511190960.3273210293110.1571850522630.6274591584720.1011841108790.513434912015-16.625568123717.7529654492-63.7063196325
97.38404281434-1.960680523660.6876546041015.12800018738-1.377041722055.422533567260.107305807598-0.24468078209-1.324458845270.8376357201170.967979376828-0.60402854733-1.105059973850.0451978724662-0.1754701491880.5699000083980.0144834640496-0.05427475286550.302416484691-0.04131047344410.675341943713-9.476385720328.50059512812-53.5027226008
103.59171166843-0.246627302746-1.940201274351.685238160970.6640510536931.97024132056-0.345263347887-0.477627186084-0.2617104350730.8003166062880.3304911039730.408070911097-0.844157768468-0.992779244699-0.2386393795271.179883309750.6386468313310.2221737295781.534988155710.2776886176810.810810847463-29.812989338614.7523230429-42.5135515705
114.37589818881-0.799574264114-2.181661109143.482702256290.619557774663.072477858110.3538122758270.5675900564020.360365937670.481048389292-0.20059804040.384052620911-0.0692688637189-0.1243743867070.03482822827030.9083414176690.3429030939070.2623835480651.553431895430.3114055836710.887135418928-29.38450095816.804683384-38.1092847176
124.669483186210.476259800933-1.083567636313.85913691720.3277607327785.38587009351-0.1512346269250.5475761180920.525920465693-0.2143015301970.5191294950760.863525502955-0.453735376693-0.218260329353-0.438909508690.553344868301-0.113940423005-0.1496198932120.4977430183250.2731024247580.7596243738-45.338525386-28.568524037533.5887888857
132.750242283232.16264685135-3.801913869971.37920093616-1.949365874254.72787855458-0.5719506640480.767293438028-0.716647563896-1.511820037010.1644681147940.04462726793482.14413896776-0.9024256765890.9701763514651.379272664920.01098178092720.0793207717870.6009115055180.02138885124190.648400069554-16.3563632198-29.21431240338.88524390755
144.635985366651.899175669290.1969524146733.399919244761.967692112333.79747943636-0.68663670561-0.414157790831-0.038613291525-0.5314808165570.248119762379-0.08075820370971.52533700478-0.5554098751770.3239955171071.21712237837-0.1792098373660.08083991468820.8436876636230.09140731285590.50692479931-7.70292641134-17.1182273773-4.12607761271
155.55569097794-0.515489963845-1.095473278693.76460529827-1.111639780855.168922363590.07904218244280.1935675537260.160583376928-1.18516184032-0.00157721072893-1.54669402304-1.066143884650.111141396195-0.03109146966981.35962619442-0.2792580428050.4569787184271.094270806690.03492938529950.95454855334216.5061813522.29940311581-12.3226222927
166.637955262150.341209946033-1.731236453126.65387152744-0.2965661228115.831777068810.87288555916-0.79706153782.12552550221-0.9521450521080.225148763835-0.0463943541265-0.1321428852510.833888705366-0.3466613373810.680364244742-0.03775102845590.04154385818130.756582432302-0.04743952517760.594799862301-17.4693105903-0.03623779840959.14924637496
179.20314380116-4.014131472081.263866600598.808455633020.5261804360675.01371695356-0.603986012217-0.2426559378990.03497818003440.46971165490.525932785646-0.1701917868040.4992083516971.03576400909-0.7006174414980.475449485605-0.2324763480530.07101923333451.31212416290.03816490122090.571724903709-15.1094602739-11.122844123612.7634480485
181.10419773283-0.129782440803-1.405931191452.766202897790.4291718781573.31401298737-0.0852798825519-0.4026945931740.08352072283281.073766644660.07411755274740.8191119042150.724394113677-0.0558655438795-0.4579793316230.725258398831-0.3691224915590.1381613963071.031563710820.0221160660610.824737423015-24.770183652-8.9026175721416.6855019737
196.329548289871.39661909144-5.631925514774.20156645511.210587327296.59062889682.2362734467-0.8394214769581.64224494655-0.661047216152-0.2520804437810.507066136151-3.1738924119-1.601876111622.32937111022-0.265559189996-0.378994741012-0.4839663307461.53691252606-0.2937552826570.935937774728-21.1711603525-2.4890172292919.1230192735
208.0703443351.68404528714-0.5857112465155.16184553005-0.4979216757338.908979187870.158119730371-0.915014650282-0.09962292218190.333458701061-0.140508857425-0.1042522586931.33592123135-0.577073554131-0.426223301060.706144062243-0.2137696952070.007364788939080.9691810818820.007169890001020.544756390499-16.3595361507-6.6178337818211.6389445379
214.45982821891.76865969941-3.672616750231.89847805445-2.459087635397.050067789480.7174925326030.05426923295461.84003465228-0.0770637372756-0.1992913591290.597753484642-0.914216109995-0.121284966482-0.6733369358280.894757527918-0.01458193096240.3990832364621.01695398665-0.1410584961961.049344184480.8299431048216.76871496955-0.584272858037
221.991576735530.0307859746236-0.6150560128573.83871214246-1.158219797532.431907025850.617120124114-0.6787036744690.607555215615-0.278861173947-0.194119304930.289119754724-0.570077080854-0.0348767097553-0.6916356474080.816478228983-0.2153053006960.05899158412180.987975704420.01355636189410.978178106829-0.9953831687593.31736812456-9.86128017786
233.394779516150.7019646085471.045158836126.06884125266-2.227202713751.398589359450.622474330947-1.006454333231.53546475228-1.621660411780.0355941604683-0.466972098827-2.29318603101-1.52322661199-1.031965118371.513488440710.1232929991890.2219992697551.195762377860.1223139220641.40506056836-8.495370275098.90015663869-4.22502438572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 11 through 130 )
2X-RAY DIFFRACTION2chain 'C' and (resid 131 through 241 )
3X-RAY DIFFRACTION3chain 'C' and (resid 242 through 343 )
4X-RAY DIFFRACTION4chain 'D' and (resid 4 through 17 )
5X-RAY DIFFRACTION5chain 'D' and (resid 18 through 41 )
6X-RAY DIFFRACTION6chain 'D' and (resid 42 through 54 )
7X-RAY DIFFRACTION7chain 'D' and (resid 55 through 70 )
8X-RAY DIFFRACTION8chain 'D' and (resid 71 through 95 )
9X-RAY DIFFRACTION9chain 'D' and (resid 96 through 107 )
10X-RAY DIFFRACTION10chain 'D' and (resid 108 through 146 )
11X-RAY DIFFRACTION11chain 'D' and (resid 147 through 224 )
12X-RAY DIFFRACTION12chain 'A' and (resid 8 through 130 )
13X-RAY DIFFRACTION13chain 'A' and (resid 131 through 172 )
14X-RAY DIFFRACTION14chain 'A' and (resid 173 through 286 )
15X-RAY DIFFRACTION15chain 'A' and (resid 287 through 343 )
16X-RAY DIFFRACTION16chain 'B' and (resid 5 through 34 )
17X-RAY DIFFRACTION17chain 'B' and (resid 35 through 46 )
18X-RAY DIFFRACTION18chain 'B' and (resid 47 through 62 )
19X-RAY DIFFRACTION19chain 'B' and (resid 63 through 82 )
20X-RAY DIFFRACTION20chain 'B' and (resid 83 through 115 )
21X-RAY DIFFRACTION21chain 'B' and (resid 116 through 141 )
22X-RAY DIFFRACTION22chain 'B' and (resid 142 through 205 )
23X-RAY DIFFRACTION23chain 'B' and (resid 206 through 225 )

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