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- PDB-8r21: Alpha-1-antitrypsin (Ile340Trp) in the native conformation -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8r21
TitleAlpha-1-antitrypsin (Ile340Trp) in the native conformation
ComponentsAlpha-1-antitrypsin
KeywordsPROTEIN BINDING / Antitrypsin / protease inhibitor / serpin / mutant / deficiency / small molecule
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protease binding / : / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsAldobiyan, I. / Lee, H.J. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V034243/1 United Kingdom
Other governmentNIHR investigator award to DAL
Other privateAlpha-1 Foundation to JAI 1036784
CitationJournal: To be published
Title: Structural determinants of instability in alpha-1-antitrypsin
Authors: Aldobiyan, I. / Lee, H.J. / Irving, J.A. / Lomas, D.A.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-antitrypsin
B: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)91,3702
Polymers91,3702
Non-polymers00
Water18010
1
A: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,6851
Polymers45,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,6851
Polymers45,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.450, 113.450, 136.743
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 24 through 25 and (name N...
d_2ens_1(chain "B" and (resid 24 through 25 or resid 28...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNLYSLYSAA24 - 2534 - 35
d_12PROPROPROPROAA2838
d_13LEULEUPHEPHEAA30 - 3540 - 45
d_14LEULEUTYRTYRAA37 - 3847 - 48
d_15ALAALAALAALAAA4252
d_16ILEILEPROPROAA50 - 5460 - 64
d_17ILEILEALAALAAA57 - 6267 - 72
d_18LEULEUTHRTHRAA64 - 6874 - 78
d_19ALAALAALAALAAA7080
d_110THRTHRASPASPAA72 - 7482 - 84
d_111ILEILEGLYGLYAA76 - 7986 - 89
d_112GLUGLUGLUGLUAA8696
d_113ALAALAGLNGLNAA90 - 91100 - 101
d_114HISHISGLNGLNAA93 - 97103 - 107
d_115LEULEULEULEUAA100110
d_116THRTHRTHRTHRAA114124
d_117GLYGLYGLYGLYAA117127
d_118PHEPHESERSERAA119 - 121129 - 131
d_119LEULEULEULEUAA124134
d_120LYSLYSLEULEUAA129 - 131139 - 141
d_121TYRTYRTYRTYRAA138148
d_122ALAALAALAALAAA142152
d_123THRTHRVALVALAA144 - 145154 - 155
d_124PHEPHEPHEPHEAA147157
d_125ILEILEILEILEAA157167
d_126VALVALVALVALAA161171
d_127GLYGLYGLYGLYAA164174
d_128GLNGLNILEILEAA166 - 169176 - 179
d_129ARGARGTHRTHRAA178 - 180188 - 190
d_130PHEPHEALAALAAA182 - 183192 - 193
d_131VALVALPHEPHEAA185 - 190195 - 200
d_132LYSLYSGLUGLUAA193 - 195203 - 205
d_133PROPROPROPROAA197207
d_134THRTHRTHRTHRAA203213
d_135GLUGLUHISHISAA206 - 209216 - 219
d_136THRTHRTHRTHRAA214224
d_137VALVALMETMETAA216 - 221226 - 231
d_138GLYGLYMETMETAA225 - 226235 - 236
d_139ASNASNASNASNAA228238
d_140SERSERSERSERAA236 - 237246 - 247
d_141VALVALVALVALAA239249
d_142LEULEULEULEUAA241251
d_143LYSLYSLYSLYSAA243253
d_144THRTHRPROPROAA249 - 255259 - 265
d_145LEULEULEULEUAA260270
d_146LEULEUGLUGLUAA263 - 264273 - 274
d_147LEULEULEULEUAA286296
d_148LEULEUGLYGLYAA288 - 295298 - 305
d_149TYRTYRASPASPAA297 - 298307 - 308
d_150SERSERGLYGLYAA301 - 304311 - 314
d_151GLYGLYVALVALAA307 - 311317 - 321
d_152SERSERSERSERAA313323
d_153GLYGLYALAALAAA315 - 316325 - 326
d_154LEULEULEULEUAA318328
d_155VALVALVALVALAA321331
d_156PROPROLEULEUAA326 - 327336 - 337
d_157LEULEUSERSERAA329 - 330339 - 340
d_158ALAALATRPTRPAA332 - 340342 - 350
d_159VALVALVALVALAA364374
d_160PHEPHEPHEPHEAA366376
d_161PROPROPHEPHEAA369 - 372379 - 382
d_162GLUGLUGLUGLUAA376386
d_163LYSLYSLYSLYSAA380390
d_164PROPROPROPROAA382392
d_165METMETTHRTHRAA385 - 392395 - 402
d_21ASNASNLYSLYSBB24 - 2534 - 35
d_22PROPROPROPROBB2838
d_23LEULEUPHEPHEBB30 - 3540 - 45
d_24LEULEUTYRTYRBB37 - 3847 - 48
d_25ALAALAALAALABB4252
d_26ILEILEPROPROBB50 - 5460 - 64
d_27ILEILEALAALABB57 - 6267 - 72
d_28LEULEUTHRTHRBB64 - 6874 - 78
d_29ALAALAALAALABB7080
d_210THRTHRASPASPBB72 - 7482 - 84
d_211ILEILEGLYGLYBB76 - 7986 - 89
d_212GLUGLUGLUGLUBB8696
d_213ALAALAGLNGLNBB90 - 91100 - 101
d_214HISHISGLNGLNBB93 - 97103 - 107
d_215LEULEULEULEUBB100110
d_216THRTHRTHRTHRBB114124
d_217GLYGLYGLYGLYBB117127
d_218PHEPHESERSERBB119 - 121129 - 131
d_219LEULEULEULEUBB124134
d_220LYSLYSLEULEUBB129 - 131139 - 141
d_221TYRTYRTYRTYRBB138148
d_222ALAALAALAALABB142152
d_223THRTHRVALVALBB144 - 145154 - 155
d_224PHEPHEPHEPHEBB147157
d_225ILEILEILEILEBB157167
d_226VALVALVALVALBB161171
d_227GLYGLYGLYGLYBB164174
d_228GLNGLNILEILEBB166 - 169176 - 179
d_229ARGARGTHRTHRBB178 - 180188 - 190
d_230PHEPHEALAALABB182 - 183192 - 193
d_231VALVALPHEPHEBB185 - 190195 - 200
d_232LYSLYSGLUGLUBB193 - 195203 - 205
d_233PROPROPROPROBB197207
d_234THRTHRTHRTHRBB203213
d_235GLUGLUHISHISBB206 - 209216 - 219
d_236THRTHRTHRTHRBB214224
d_237VALVALMETMETBB216 - 221226 - 231
d_238GLYGLYMETMETBB225 - 226235 - 236
d_239ASNASNASNASNBB228238
d_240SERSERSERSERBB236 - 237246 - 247
d_241VALVALVALVALBB239249
d_242LEULEULEULEUBB241251
d_243LYSLYSLYSLYSBB243253
d_244THRTHRPROPROBB249 - 255259 - 265
d_245LEULEULEULEUBB260270
d_246LEULEUGLUGLUBB263 - 264273 - 274
d_247LEULEULEULEUBB286296
d_248LEULEUGLYGLYBB288 - 295298 - 305
d_249TYRTYRASPASPBB297 - 298307 - 308
d_250SERSERGLYGLYBB301 - 304311 - 314
d_251GLYGLYVALVALBB307 - 311317 - 321
d_252SERSERSERSERBB313323
d_253GLYGLYALAALABB315 - 316325 - 326
d_254LEULEULEULEUBB318328
d_255VALVALVALVALBB321331
d_256PROPROLEULEUBB326 - 327336 - 337
d_257LEULEUSERSERBB329 - 330339 - 340
d_258ALAALATRPTRPBB332 - 340342 - 350
d_259VALVALVALVALBB364374
d_260PHEPHEPHEPHEBB366376
d_261PROPROPHEPHEBB369 - 372379 - 382
d_262GLUGLUGLUGLUBB376386
d_263LYSLYSLYSLYSBB380390
d_264PROPROPROPROBB382392
d_265METMETTHRTHRBB385 - 392395 - 402

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Components

#1: Protein Alpha-1-antitrypsin


Mass: 45684.797 Da / Num. of mol.: 2 / Mutation: I340W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1 / Plasmid: pQE30 / Details (production host): T5 promoter / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue / References: UniProt: P01009
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.59 % / Description: Dipyramidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 0.1M SPG (succinate-phosphate-glycine) pH 5.25, 17.5% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2018 / Details: Compound refractive lenses
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.878→98.251 Å / Num. obs: 19154 / % possible obs: 81.2 % / Redundancy: 10.7 % / Biso Wilson estimate: 69.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.067 / Rrim(I) all: 0.223 / Net I/σ(I): 9.8
Reflection shellResolution: 2.878→3.071 Å / Redundancy: 12.1 % / Rmerge(I) obs: 2.298 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 958 / CC1/2: 0.42 / Rpim(I) all: 0.684 / Rrim(I) all: 2.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
STARANISO2.3.94data scaling
Aimless0.7.13data scaling
XDS20180808data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→98.25 Å / SU ML: 0.4098 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2422 876 4.57 %
Rwork0.1974 18272 -
obs0.1994 19148 81.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.35 Å2
Refinement stepCycle: LAST / Resolution: 2.88→98.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 0 10 5422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225545
X-RAY DIFFRACTIONf_angle_d0.46927561
X-RAY DIFFRACTIONf_chiral_restr0.0402909
X-RAY DIFFRACTIONf_plane_restr0.0033962
X-RAY DIFFRACTIONf_dihedral_angle_d13.90381885
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.332016348911 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.060.4202470.32767X-RAY DIFFRACTION20.97
3.06-3.290.33371530.28943137X-RAY DIFFRACTION85.41
3.29-3.630.30851340.24643353X-RAY DIFFRACTION89.27
3.63-4.150.26081830.19553347X-RAY DIFFRACTION90.89
4.15-5.230.19541730.16133771X-RAY DIFFRACTION99.65
5.23-98.250.21331860.183897X-RAY DIFFRACTION99.61
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)
14.15855540835-0.7320481727622.545178223786.198231305221.746797763458.40234675523-0.2200042156630.109675809564-0.7267337015750.2631144767970.474250308692-0.0057454520313-0.03007797900140.3197185163180.03790027381140.2939749027570.03219544338470.02728985711520.4067048532960.04616302241450.482058599749-30.4325035033-35.5271585827-1.72167761648
21.56030283309-0.3584664387811.124855975642.80987005416-0.3849684248215.92759126820.09439663434150.0234446146572-0.366653877089-0.147881038009-0.194988566120.814427077412-0.00431635617284-0.7587028413160.005033915386210.3262753436310.00363934596726-0.1410070014430.547155760235-0.03251918386530.785639788856-45.309507924-29.690138432-6.64366342081
33.26642367631-0.393123661385-1.912594838755.681751032511.069481277083.37751786238-0.10724170748-0.485765117409-0.07299676904130.7285989520260.1955697766620.1838829403770.06738213039740.0023858908545-0.09325615956850.330921734162-0.0129679350772-0.05691018952430.3814794355110.1157807577090.324849073072-30.5898323331-28.598526219919.8970370077
41.88556043142-0.08055769458420.8163726889991.672093873530.6668352984916.005855144820.1901988934610.0339009001477-0.251530023641-0.0606201702429-0.1055329920270.1840144266590.1357419092350.0728986303418-0.1850043963580.243105011832-0.0582661782859-0.06964520710240.2737116107620.04178887713130.548122327824-33.5899834473-30.54056482540.287316393385
54.825361595551.20603424755-0.7419412261573.469714045410.946683195327.23424462994-0.0351523006677-0.681203207-0.3864986975750.481166272308-0.1021482654840.3733732787350.413061890919-0.918004691810.0888608262220.415485136491-0.029362111204-0.0335641095130.5546793683830.1560619777470.422795476222-35.3309979745-30.615718723318.2105656268
61.84666973824-1.318371636641.776444702523.35486399916-1.321630847042.78643076527-0.02731596287430.3206237321250.274364696707-0.709784329935-0.108436435514-0.0251349476402-1.09615599361-0.9520556817140.02718244964151.138975469630.0975125503963-0.1459065990550.4824891327770.03426080477130.585068978531-29.09276052322.16080022698-11.3103420814
71.54194272760.01632511526361.462155248860.002142139990140.02707956378793.04100080468-0.1092665647450.09662160365050.564561128661-0.589774182807-0.326938149710.236116878706-1.07464807886-0.304833299966-0.4326178574662.393514073190.756335580195-0.5771637936680.5603285365450.2336863284320.741738010509-35.20407736595.54259153775-24.7849094918
81.03322926983-1.96877221023-0.2220900227183.733919358450.6040652927835.622749087210.02578792052460.1255875376920.650322818543-1.10792269290.38361538803-0.95727266882-1.652566358061.148580598570.1596446823661.4644768241-0.2058803049060.3236818062260.744750245120.08502146065580.672055505589-16.20704735823.78937971128-19.3268962115
93.50021233418-0.6553774340960.2663538110333.865476572050.6826403754987.78916833619-0.0105645717730.4116752482890.157190879556-2.22540811172-0.0951445204428-0.0372158818638-1.069096794990.574303851151-0.1807404009181.400358071510.04732768252090.03595205654030.67722513272-0.009275890171890.658718938958-19.5477639681-8.39613581921-30.0580278331
101.38901126023-0.1126709631870.3370276726563.239368188452.693376093493.320362953460.04487276081850.01895131712530.24373996332-0.7565521423830.4591793738-0.417347719656-1.007041286320.520324202181-0.4977610094180.66896661896-0.1348928157760.1460607263120.4162676255010.03396007579340.55143258571-18.1576333824-1.06188495486-0.539155081414
112.25799681666-0.4155394770581.271726691773.048708900660.3435787093292.828938783820.260034155254-0.2260175425121.02474785938-0.952725351189-0.1780720558580.0251058005205-1.39146598553-0.5787953402840.01564212704831.15143403730.0734112910350.1658214156170.510080511082-0.06534082076750.718346204274-26.357166293512.35770836164.96057522847
122.21099990195-0.3261263903580.438327099952.504598884441.404515125884.97542907930.1490999925970.271798685398-0.161622709044-0.918597867214-0.2696759823470.278715050133-0.419675933765-0.9059475934080.2366097077321.236156443610.0590053362688-0.03531578107080.4355292471130.0645896545830.5900296946-31.5075898487-6.81396612907-19.1699814754
131.76097271018-0.906673639155-1.019537834120.8439380101440.6546933123452.51126957870.12016508383-0.2934544793920.230478057979-0.883500894150.22217862463-0.538130947428-0.7837064844450.506508133881-0.1981101958610.812000730853-0.1041952990820.173640579040.485757758260.01233807715750.538602221619-17.45037615351.12381903552-2.38826796543
144.241255852290.9982015195840.3459176861557.43515656295-2.667941139493.136444874610.2765353236380.3412599810810.100304148547-1.58289938340.416682403115-0.6742492183630.5307761423620.7294489846-0.4950152253160.887289880863-0.05605852083080.1232807681330.372744103109-0.06678627683670.514367493624-22.19159114954.266784905832.18671392636
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 44 )AA24 - 441 - 21
22chain 'A' and (resid 45 through 199 )AA45 - 19922 - 173
33chain 'A' and (resid 200 through 255 )AA200 - 255174 - 229
44chain 'A' and (resid 256 through 340 )AA256 - 340230 - 314
55chain 'A' and (resid 341 through 393 )AA341 - 393315 - 365
66chain 'B' and (resid 24 through 67 )BB24 - 671 - 44
77chain 'B' and (resid 68 through 88 )BB68 - 8845 - 65
88chain 'B' and (resid 89 through 121 )BB89 - 12166 - 98
99chain 'B' and (resid 122 through 149 )BB122 - 14999 - 126
1010chain 'B' and (resid 150 through 255 )BB150 - 255127 - 232
1111chain 'B' and (resid 256 through 290 )BB256 - 290233 - 267
1212chain 'B' and (resid 291 through 325 )BB291 - 325268 - 302
1313chain 'B' and (resid 326 through 361 )BB326 - 361303 - 330
1414chain 'B' and (resid 362 through 394 )BB362 - 394331 - 363

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