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- PDB-7tuh: Crystal structure of anti-tapasin PaSta2-Fab -

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Basic information

Entry
Database: PDB / ID: 7tuh
TitleCrystal structure of anti-tapasin PaSta2-Fab
Components
  • PaSta2 Fab heavy chain
  • PaSta2 Fab kappa light chain
KeywordsIMMUNE SYSTEM / PaSta / Fab / Antibody / IgG / MHC-I / HLA / peptide loading complex / PLC / antigen presentation / immune response
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJiang, J. / Natarajan, K. / Taylor, D.K. / Boyd, L.F. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation.
Authors: Jiang, J. / Taylor, D.K. / Kim, E.J. / Boyd, L.F. / Ahmad, J. / Mage, M.G. / Truong, H.V. / Woodward, C.H. / Sgourakis, N.G. / Cresswell, P. / Margulies, D.H. / Natarajan, K.
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PaSta2 Fab heavy chain
L: PaSta2 Fab kappa light chain
A: PaSta2 Fab heavy chain
B: PaSta2 Fab kappa light chain


Theoretical massNumber of molelcules
Total (without water)98,1434
Polymers98,1434
Non-polymers00
Water2,522140
1
H: PaSta2 Fab heavy chain
L: PaSta2 Fab kappa light chain


Theoretical massNumber of molelcules
Total (without water)49,0722
Polymers49,0722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area19900 Å2
MethodPISA
2
A: PaSta2 Fab heavy chain
B: PaSta2 Fab kappa light chain


Theoretical massNumber of molelcules
Total (without water)49,0722
Polymers49,0722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-23 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.104, 62.127, 128.462
Angle α, β, γ (deg.)90.000, 90.036, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody PaSta2 Fab heavy chain


Mass: 24792.748 Da / Num. of mol.: 2 / Fragment: Variable and Constant CH1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21b / Cell line (production host): Expi 293S / Production host: Homo sapiens (human)
#2: Antibody PaSta2 Fab kappa light chain


Mass: 24278.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21b / Cell line (production host): Expi 293S / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
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: 2 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 14% PEG 6000, 0.1M Na. Cacodylate / PH range: 5.5-8.5

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Data collection

DiffractionMean temperature: 273 K / Ambient temp details: LN blow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→64.23 Å / Num. obs: 34309 / % possible obs: 98.98 % / Redundancy: 5.8 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1086 / Rpim(I) all: 0.049 / Rrim(I) all: 0.1195 / Net I/σ(I): 8.66
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 0.78 / Num. unique obs: 3406 / CC1/2: 0.3 / CC star: 0.679 / Rpim(I) all: 0.866 / % possible all: 98.81

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UYL

2uyl


Resolution: 2.3→64.23 Å / Cross valid method: FREE R-VALUE / σ(F): 46.53 / Phase error: 26.1484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 1734 5.05 %
Rwork0.2181 32575 -
obs0.2214 34309 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→64.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 0 140 6606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226628
X-RAY DIFFRACTIONf_angle_d0.53349046
X-RAY DIFFRACTIONf_chiral_restr0.04131033
X-RAY DIFFRACTIONf_plane_restr0.00391143
X-RAY DIFFRACTIONf_dihedral_angle_d4.2874912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.31491420.28732703X-RAY DIFFRACTION93.79
2.37-2.440.32961420.28862697X-RAY DIFFRACTION94.4
2.44-2.530.32421410.28632670X-RAY DIFFRACTION94.11
2.53-2.630.34071440.28452748X-RAY DIFFRACTION94.5
2.63-2.750.32661430.2832708X-RAY DIFFRACTION94
2.75-2.90.28831410.26832669X-RAY DIFFRACTION93.45
2.9-3.080.27571410.25722680X-RAY DIFFRACTION93.15
3.08-3.320.24711420.25112714X-RAY DIFFRACTION94.47
3.32-3.650.26571440.22642726X-RAY DIFFRACTION94.49
3.65-4.180.20521440.19762746X-RAY DIFFRACTION93.94
4.18-5.270.16151440.15412732X-RAY DIFFRACTION94.27
5.27-64.230.20421480.18522800X-RAY DIFFRACTION93.9
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)
10.642257377101-0.600475613417-0.5091409688673.651801882411.618533468352.04864915452-0.147919157824-0.3582362184380.3863256863960.6858162612930.150515866584-0.7911722500780.305206015214-0.2554019378970.0477084673450.4905143112810.111156971646-0.200052423152-0.0461370907912-0.05608742975030.554559228756-6.9578632376622.424760590831.2616056315
22.57234628253-1.026063045731.718223922840.803738091668-0.7190639411871.2799254491-0.04264097735180.03760050644240.04896687466626.56895350957E-60.09439948143910.06152560039370.1531936341250.155214592553-0.00685767137040.310836272539-0.02099434181810.08826609467560.150296917337-0.01293000862680.27374281474-14.380481988720.44246609618.3882198611
35.01525038150.528307336381-1.506977492392.619334844081.950479407792.19047477599-0.4550293740840.5625504136130.145424695527-0.0968788615904-0.05626070348010.427755525465-0.143726654859-0.1724833969610.2917091223910.636516394647-0.266854690209-0.3889306563090.1791858242390.08861273976620.592359054257-40.576529875823.8884379433-8.85298406709
41.908328225850.682087715913-0.4814883985931.825080506370.2932152664810.377424527853-0.0557923606640.02446826691530.260718028985-0.3815133483490.05982406183090.33041649457-0.156626028120.0641630790606-0.00942613307210.584327978749-0.0104554827404-0.1313842524020.229814166362-0.01791763915140.283093133488-27.09820635721.6231351112-3.12247409404
55.66621224722-0.1108529167165.720243780330.157335456982-0.5381691987037.44698979749-0.4792502855030.292836912232-0.282003934753-0.1870736403310.522404184075-0.0626139548173-0.7956943939780.7312513040220.1176008268980.60705221792-0.066413552190.02538473345410.3324054847630.005640453219450.434301621538-22.370432177717.472053504-9.51997566604
68.22190124418-6.143098418246.138423167248.01277962063-7.216268509877.43242152778-0.376749176683-0.38348477892-0.2432572606361.514278880340.3535273178250.480335202161-0.933003118481-0.293080165199-0.005145518679710.4882485853450.03168371899030.06391431996010.1783434424730.02879074522190.324711172014-30.546115950230.282580498831.0073234036
71.474003954420.5436039366070.3816317536361.7929372320.05140727858832.23990804283-0.005586641412330.01358133532980.238253546610.02095790561970.03808322639820.00963709891459-0.116259499033-0.0251074813635-0.0240408078950.388183018940.009855621461470.01817713890810.1717651809250.01006084311730.309372870517-22.345575448438.576128754233.4215862883
82.24730498324-0.0135612680732.067729363511.469592015031.24554313094.3698011796-0.162071735873-0.02095171530610.2464675203080.1624433815110.1343712664390.33983412542-0.169252971039-0.0431269706920.05887380273470.2929323335370.02389117549040.07314867384920.193982996620.02518323335860.37563144474-27.798045402335.98132828928.1071981067
90.6290341843420.420886867752-0.8558795260176.703098560541.25325136651.48401796263-0.304968755475-0.125162043623-0.175438096448-0.1247694266550.4091288168450.1262475226410.2049846397810.137966944912-0.04116881561160.4807771473110.0214633401269-0.1421741591080.2817028164470.09495894394290.427401861387-38.202233535216.97338293544.32552057092
100.3517212304490.616066327539-0.8369110967451.05825297936-1.430004232291.90568211034-0.02334294804840.328295183842-0.878484551248-0.5168283280140.9572796289580.4609780235890.433686823979-0.282394620824-0.1476474428190.515915285296-0.041775986278-0.3226656610840.555075405588-0.2903344576380.948237846284-46.75795955811.18588075761.58742008084
110.4530056325850.627137531022-0.8348238116041.0167141001-1.367243563441.857530235720.258519661950.497105519109-0.331473559956-0.06686524420090.2011331953490.4889374826110.0457893708075-0.4691980765590.5612234820890.346730699323-0.112050820108-0.2921275002510.570271254866-0.06646640050930.749168061605-49.184878861619.31305769881.37034433254
122.134940977551.1858088896-0.4426312695995.17872224191.790834424153.304173287840.04458877653040.00826692111181-0.115981968353-0.3837581306840.177340846949-0.727506808325-0.08639016870.22218609187-0.1909425775080.365136252364-0.0327719277888-0.002100728455360.1524610387290.0001500063322290.39623610390817.52051889628.1751814650636.8797503498
131.04574757957-0.120754877316-1.224620770191.081395552661.126591464543.55105594423-0.0446248040123-0.141181055428-0.1001023079580.02707714374690.08256482899730.02058129237310.06751489640790.013449282402-0.0580214430560.3783316413390.0457892853698-0.03231805519370.1244075958740.06728943301750.2745882454622.168651656637.8814793655255.2260280964
141.96151588581.25080168886-1.678219100361.179893659-1.621330724722.38370020338-0.00770484385651-0.0331599573613-0.3123886537890.1239517941550.02389038766930.06836868921550.1685837805960.1087285023690.01060533489960.5047811395510.05135962527580.006765922424010.198549205056-0.07464563718530.297230659379-0.451439121647.4381577859666.6841092596
152.694816135511.19757054777-0.4642543790310.818371135614-0.5184800749683.003444393150.00053000139748-0.118953816870.2370753101850.106835560980.1079993389760.306100829716-0.3528443353950.145358124964-0.1161465106510.4772086895730.07327052348790.1083227738680.179900609941-0.01888094679460.304900579551-2.5417147704710.174821053169.5297879497
162.717326873720.9422247426690.7940380416392.79872338569-2.016360806534.27897162844-0.187136965565-0.0290537666075-0.231027999694-0.1865426185520.09516679125730.122113952914-0.0425619989096-0.1443330014080.07908592317440.3300302259790.0293901977890.04376586535860.134863701513-0.05146863307770.315353337396-0.0223252432574-7.8108106959731.7332309996
171.075797169280.195562356631-1.200207067170.6546249635660.09495870592182.25030445733-0.01733061773090.02955372917090.01750576693620.04727544772630.1453825489430.09002500112460.0489911717908-0.162556220778-0.1097710519590.3295015631470.07134700217850.05581208054340.2325349154760.0519836151280.300407461394-9.642364308996.4129330576552.8254810564
181.964022633940.481370864341-1.142194741252.043030264920.8552718705372.33829968355-0.07154433270.3027706895340.504474204609-0.158749841190.0416481756752-0.110556269483-0.523685008738-0.08371458343550.03948631371280.4424825274070.000321862686083-0.01509015718410.2337208207990.09393089064970.435040349072-13.53593340579.8914433132855.7053982824
191.76431654472-0.1111094292630.5011895145896.67718724041.753264203951.088464685990.04335115730540.1225791982110.476595389171-0.1941603088840.03754023723120.616935218322-0.446017009393-0.23342247212-0.07597484325310.5564333798010.06737935760960.1657291361480.3032978423550.05855833090720.42694570252-19.908599326917.29512934962.2747946894
201.57974764745-0.490045234675-0.3458425082422.20942249748-0.7820502942540.458918196913-0.2467958054880.3457969991750.445508927167-0.832454269720.704288763973-0.665174252163-0.05660688774760.279459048659-0.2606899482710.472071915841-0.01469894500910.1463088139330.235399248246-0.1401243138860.532778549177-5.0672379323720.917212560219.8059828579
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 83 )AC26 - 8325 - 79
22chain 'A' and (resid 84 through 128 )AC84 - 12880 - 124
33chain 'A' and (resid 129 through 141 )AC129 - 141125 - 131
44chain 'A' and (resid 142 through 203 )AC142 - 203132 - 193
55chain 'A' and (resid 204 through 217 )AC204 - 217194 - 207
66chain 'B' and (resid 1 through 13 )BD1 - 131 - 13
77chain 'B' and (resid 14 through 67 )BD14 - 6714 - 67
88chain 'B' and (resid 68 through 119 )BD68 - 11968 - 119
99chain 'B' and (resid 120 through 192 )BD120 - 192120 - 192
1010chain 'B' and (resid 193 through 204 )BD193 - 204193 - 204
1111chain 'B' and (resid 205 through 217 )BD205 - 217205 - 217
1212chain 'H' and (resid 1 through 98 )HA1 - 981 - 98
1313chain 'H' and (resid 99 through 141 )HA99 - 14199 - 141
1414chain 'H' and (resid 142 through 169 )HA142 - 169142 - 169
1515chain 'H' and (resid 170 through 216 )HA170 - 216170 - 216
1616chain 'L' and (resid 1 through 96 )LB1 - 961 - 96
1717chain 'L' and (resid 97 through 152 )LB97 - 15297 - 152
1818chain 'L' and (resid 153 through 180 )LB153 - 180153 - 180
1919chain 'L' and (resid 181 through 217 )LB181 - 217181 - 217
2020chain 'A' and (resid 2 through 25 )AC2 - 251 - 24

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