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- PDB-9azr: Lineage 860 UCA Fab bound to A/Massachusetts/1/1990 hemagglutinin head -

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Basic information

Entry
Database: PDB / ID: 9azr
TitleLineage 860 UCA Fab bound to A/Massachusetts/1/1990 hemagglutinin head
Components
  • Hemagglutinin HA1 chain
  • Lineage 860 UCA Fab heavy chain
  • Lineage 860 UCA Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / influenza / hemagglutinin / UCA / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMaurer, D.P. / Schmidt, A.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI146779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI089618 United States
CitationJournal: Immunity / Year: 2025
Title: Antigenic drift expands influenza viral escape pathways from recalled humoral immunity.
Authors: Maurer, D.P. / Vu, M. / Schmidt, A.G.
History
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Hemagglutinin HA1 chain
H: Lineage 860 UCA Fab heavy chain
L: Lineage 860 UCA Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1474
Polymers73,9263
Non-polymers2211
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-23 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.543, 71.863, 65.402
Angle α, β, γ (deg.)90.000, 104.870, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11H-333-

HOH

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 25390.203 Da / Num. of mol.: 1 / Fragment: head domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Massachusetts/1/1990(H1N1) / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q07775
#2: Antibody Lineage 860 UCA Fab heavy chain


Mass: 25839.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Lineage 860 UCA Fab light chain


Mass: 22695.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4k, 200 mM imidazole, pH 7.4, HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→48.94 Å / Num. obs: 39860 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 43.62 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.35
Reflection shellResolution: 2.3→2.44 Å / Num. unique obs: 5923 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.94 Å / SU ML: 0.3219 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.4955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2703 2006 5.04 %
Rwork0.2285 37806 -
obs0.2306 39812 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 14 217 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035172
X-RAY DIFFRACTIONf_angle_d0.54637055
X-RAY DIFFRACTIONf_chiral_restr0.0444770
X-RAY DIFFRACTIONf_plane_restr0.0043907
X-RAY DIFFRACTIONf_dihedral_angle_d4.6282712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3441190.32552164X-RAY DIFFRACTION79.3
2.36-2.420.37151570.30782719X-RAY DIFFRACTION99.31
2.42-2.490.36541290.30232727X-RAY DIFFRACTION98.99
2.49-2.570.34151470.30892703X-RAY DIFFRACTION99.23
2.57-2.660.38171460.33772715X-RAY DIFFRACTION99.51
2.66-2.770.39171480.31152760X-RAY DIFFRACTION99.55
2.77-2.90.32071400.28322727X-RAY DIFFRACTION99.69
2.9-3.050.32561480.28022682X-RAY DIFFRACTION98.99
3.05-3.240.3481390.26452750X-RAY DIFFRACTION98.4
3.24-3.490.28961460.24752745X-RAY DIFFRACTION99.9
3.49-3.840.26841460.22052760X-RAY DIFFRACTION99.79
3.84-4.40.22521490.18882749X-RAY DIFFRACTION99.49
4.4-5.540.20121400.16072772X-RAY DIFFRACTION99.39
5.54-48.940.19911520.17672833X-RAY DIFFRACTION99.5
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)
11.9966277538-1.14581004137-0.2668764643630.7251584989470.03440351729240.6531585166060.366819833804-0.240265373712-2.089112092850.972698342241-0.0775417219927-0.5281393754250.466615836796-0.050850453179-0.2005412155370.6624313813180.00705557062385-0.2644677141090.4818830159210.3073936212161.358324612125.9813768244-29.796223043823.9435744197
20.0780438196038-0.1160597991990.04816293103950.4580224798970.1974285435150.163838125939-0.3573352139260.71524457357-1.08261605926-0.1852577248530.166641006698-0.3792099044080.4860541849270.395553174705-9.53942520965E-50.5149727406850.000405114323113-0.01190580543280.531169572208-0.09285333474720.63801157287325.0710756002-23.518732440812.5361426975
31.92212481491-0.04439453870350.4428996476360.4788618597010.2289655067760.5397401493140.0577146190579-0.325599068828-0.07729485904030.1079472488-0.0206241040362-0.0198509782028-0.047753927205-0.03316417107553.54961290586E-50.387821129562-0.0308840916438-0.01188326194380.4561846418680.04170970319470.33477436001918.0355923574-10.163167988621.1200556358
40.412142969304-0.0948165399588-0.2078864057810.9934302463890.05177532995990.4496143965710.118744814193-0.02815008784680.06379779523470.0563177959769-0.1336370247790.02028841688860.07369169286220.0236260257208-4.46005289357E-50.3351057377860.00103732311865-0.002510828422850.3857154442130.09875049043050.34970657764121.4305164638-13.085349510616.2386285854
50.2208063767-0.211499597633-0.2336653119990.09659523872990.2940873229470.3128170891910.00262673768269-0.1057227470440.4900574395970.165548337710.01986318036990.0013926684574-0.525137340424-0.0997498045960.001026421982250.5314639200720.01680487350710.07337767769080.5051399312150.08341651694520.467516852855-18.27716050548.9373992245916.4474296309
60.5759342664140.074355781624-0.1321103344110.2593692646530.2839520245850.2727691534740.314488562261-0.00745542220156-0.7458437127050.08039756523060.352996800339-0.168906228131-0.109399277375-0.08293959764880.01315116665880.482012205575-0.01046725829650.052359388930.481489628480.0993468120990.354268961806-11.22642138331.0631320095615.5932281877
70.141669681846-0.247871608360.04079154701190.906832061847-0.4857745114080.3057707036320.0663063727177-0.0007277607602110.353369647662-0.130825572697-0.2193265210540.340493567378-0.0529379979656-0.1788692539880.000260591465270.3822552130740.008451311278840.01300543457730.471241565065-0.0139457083080.374745863049-9.840291794390.40769062587510.2466616726
81.02426634909-0.0848010824739-0.258368429760.370995788387-0.2176166503880.1881495297560.3132419918940.2957360972850.0707756765506-0.226226398470.171685693799-0.487961883892-0.360108961490.4770333777810.001120615437320.6118207183130.04760629302750.06114853949630.487672028642-0.00311355358110.453675627765-10.32686059388.176211581449.9694295575
90.33255589731-0.127207121546-0.04635161787820.240707041568-0.2171540692490.1714571208550.008660862057720.237065707579-0.357920360182-0.2328145368910.0126516011713-0.03804047938820.387106949953-0.313008047903-0.0006351702231660.5466718160240.00905821551933-0.002547834655350.546640723920.1317865460290.397685880824-19.74879737424.193146786646.45167766018
100.130020869065-0.0744487269947-0.09218745410380.145564208896-0.3241322618570.368731108609-0.22091912728-0.429180598436-0.1333518073670.1671077502610.1718938256930.08289982199650.05380088813830.1718158035150.0001155654046020.4150550055190.04083151070670.002759111863710.4781169955450.04859438357220.390828263183-6.7470596543-7.8384632001919.4824942466
110.08143491584150.09669278483280.1690045764080.1510302420550.3266350286260.404344494918-0.195608653020.4478783928590.3297237665090.06158914785870.1341453876650.369903830331-0.5871302826670.326323365268-0.003367139052170.5181746910980.1080490280020.02185466877750.4892641709080.1303012758280.498309628217-33.187945302811.12527756423.42989889347
120.244323392578-0.1235790681540.2058633869440.202727959924-0.03150059548080.4479241418220.00243561328128-0.106130583935-0.3720349477780.9034205608240.3425167292650.3476169678790.113399995418-0.4255257979040.005497533808350.44986509592-0.09507102414010.06398463151760.488019472788-0.163379602870.788062722739-57.2830864791-5.27598886011-1.98772457306
130.4441123709860.02773816397820.5011441429280.04391634376280.1587418050390.49236514768-0.2268518278420.0889541920057-0.2826048068980.112129823330.0511300777597-0.2113278279510.1140498726790.1225931856231.01688432944E-50.4729111747460.009530685788980.06363602752480.3822253445640.01721545985480.481812091569-47.76549500382.00812691735.83904755258
140.654617425302-0.5092423436910.6801815896441.00594835042-0.05009214914590.487389705571-0.1638741497670.179234820544-0.1593372723270.147354352955-0.0331301772580.263765680691-0.030862654482-0.317654065580.0001231943336730.4342509526730.003289592925670.05213379019550.364383687996-0.1169409508480.52361118957-56.20294486693.313620612845.16116848231
150.2250318860580.2423344108230.4116865242430.08751931565410.2369435414280.50417796817-0.2492718912280.317385712981-0.488739498684-0.3250146903740.3340746998520.1096772122860.744572036822-0.189210395861-0.0008007417950560.428495876138-0.00940683159915-0.01023746299520.4998037301650.09743834224650.595467655803-18.8236227601-21.480720892611.6966582849
160.2651177334460.4764793401930.3881712818630.692161803340.6631746177530.309642287757-0.2058360806840.149927793486-0.4723672969110.368867795208-0.1428191206630.536717213375-0.0924224366582-0.487237179778-0.003049991817140.3565420170420.009157558183070.01074092197130.4419703065760.1046555851140.319122554583-18.9097719191-11.285201636618.6174732341
170.2420642100570.116346920710.1031800190210.3287563873560.01206448271820.16236829232-0.0979979997408-1.08613309418-0.4577995116170.304110311032-0.1583379164380.4551063156320.504959237790.120103710111-0.00902185126430.5733769902270.0527358618381-0.007569218082210.7051785171770.1783358439990.578075556278-15.5460551305-17.16404786527.1261413149
180.6423902142230.7628040601280.2624689716460.5985218175990.4623744161520.2349348990040.216008422658-0.27279474768-0.384329536825-0.0661958899206-0.1284593522410.187659200087-0.01547360844490.05667115282110.000131494517280.4034674236320.02047263204060.02418763068060.5520682604340.1303578918410.443036243614-18.8447954317-18.873767710817.454656896
190.304718658588-0.05768086700920.2707550694830.334273343604-0.0573846344816-0.05935340468870.219125662528-0.582432545209-0.02547193464340.0162038742572-0.224746197927-0.0963946807972-0.01201966791450.04390862768215.15403244627E-50.462238283327-0.02103849266540.002543692198050.4490906957830.05328948937880.400781164353-24.7521815611-15.710553356610.4832091857
201.01181323224-0.1799578642020.1806426288260.3715322400270.4439131086590.976810967440.04951401388310.0014243121785-0.03030163089630.084661009202-0.2026918133770.0677615167231-0.09219191267610.03131335498844.81893811129E-50.3545115121750.0169374421788-0.003460518060530.363518281265-0.02023815141240.457254657648-47.1166222791-7.11025118811-3.46801009336
211.307106466670.341888515774-0.2613428903641.28757343950.1233723319680.1904800179780.120718529593-0.00184288394419-0.0453422704961-0.0380505736816-0.1245510246630.209345352723-0.3267159804510.135167844491-0.0005431216451730.3401891907290.0100025190883-0.01817051324660.407776830799-0.007209469169820.48153630133-43.0805665416-7.30377425035-3.58829502759
220.2774695310590.177283421301-0.232310055760.2981891666950.2252565341080.6799681684850.0538920359219-0.173696171259-0.421839305619-0.245511782708-0.0312862813466-0.003095465838450.4283296163410.0241535988228-0.008966541320840.3963051831720.00826225441413-0.04618284504410.418359307663-0.1590724395690.51449874897-47.0607364888-14.9530330427-8.58797278676
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 52 through 86 )EA52 - 861 - 35
22chain 'E' and (resid 87 through 108 )EA87 - 10836 - 57
33chain 'E' and (resid 109 through 213 )EA109 - 21358 - 163
44chain 'E' and (resid 214 through 263 )EA214 - 263164 - 213
55chain 'H' and (resid 1 through 28 )HC1 - 281 - 28
66chain 'H' and (resid 29 through 40 )HC29 - 4029 - 40
77chain 'H' and (resid 41 through 60 )HC41 - 6041 - 60
88chain 'H' and (resid 61 through 83 )HC61 - 8361 - 83
99chain 'H' and (resid 84 through 98 )HC84 - 9884 - 98
1010chain 'H' and (resid 99 through 119 )HC99 - 11999 - 119
1111chain 'H' and (resid 120 through 132 )HC120 - 132120 - 132
1212chain 'H' and (resid 133 through 147 )HC133 - 147133 - 147
1313chain 'H' and (resid 148 through 188 )HC148 - 188148 - 188
1414chain 'H' and (resid 189 through 227 )HC189 - 227189 - 227
1515chain 'L' and (resid 1 through 29 )LD1 - 291 - 29
1616chain 'L' and (resid 30 through 47 )LD30 - 4730 - 47
1717chain 'L' and (resid 48 through 60 )LD48 - 6048 - 60
1818chain 'L' and (resid 61 through 91 )LD61 - 9161 - 91
1919chain 'L' and (resid 92 through 115 )LD92 - 11592 - 115
2020chain 'L' and (resid 116 through 152 )LD116 - 152116 - 152
2121chain 'L' and (resid 153 through 189 )LD153 - 189153 - 189
2222chain 'L' and (resid 190 through 212 )LD190 - 212190 - 212

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