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- PDB-9mqv: Crystal structure of human 1122A11 Fab in complex with influenza ... -

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Basic information

Entry
Database: PDB / ID: 9mqv
TitleCrystal structure of human 1122A11 Fab in complex with influenza virus neuraminidase from A/Singapore/INFIMH-16-0019/2016 (H3N2)
Components
  • 1122A11 FAB IGG1 HEAVY CHAIN
  • 1122A11 FAB LAMBDA LIGHT CHAIN
  • Neuraminidase
KeywordsVIRAL PROTEIN / HYDROLASE/IMMUNE SYSTEM / HYDROLASE / IMMUNE SYSTEM / Influenza virus / neuraminidase / neutralization / substrate mimicry / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Biorxiv / Year: 2025
Title: Structure and function of a cross-neutralizing influenza neuraminidase antibody that accommodates recent N2 NA Asn245 glycosylation.
Authors: Zhu, X. / Khalil, A.M. / Piepenbrink, M.S. / Yu, W. / Ma, Y. / Martinez-Sobrido, L. / Wilson, I.A. / Kobie, J.J.
History
DepositionJan 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
H: 1122A11 FAB IGG1 HEAVY CHAIN
L: 1122A11 FAB LAMBDA LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9729
Polymers91,7163
Non-polymers3,2566
Water6,575365
1
A: Neuraminidase
H: 1122A11 FAB IGG1 HEAVY CHAIN
L: 1122A11 FAB LAMBDA LIGHT CHAIN
hetero molecules

A: Neuraminidase
H: 1122A11 FAB IGG1 HEAVY CHAIN
L: 1122A11 FAB LAMBDA LIGHT CHAIN
hetero molecules

A: Neuraminidase
H: 1122A11 FAB IGG1 HEAVY CHAIN
L: 1122A11 FAB LAMBDA LIGHT CHAIN
hetero molecules

A: Neuraminidase
H: 1122A11 FAB IGG1 HEAVY CHAIN
L: 1122A11 FAB LAMBDA LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)379,88936
Polymers366,86512
Non-polymers13,02424
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area52530 Å2
ΔGint44 kcal/mol
Surface area121970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.900, 115.900, 76.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase


Mass: 43531.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5B8WQ58, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules HL

#2: Antibody 1122A11 FAB IGG1 HEAVY CHAIN


Mass: 25572.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): ExpiCHO
#3: Antibody 1122A11 FAB LAMBDA LIGHT CHAIN


Mass: 22612.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): ExpiCHO

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Sugars , 4 types, 5 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: 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

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Non-polymers , 2 types, 366 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M tri-potassium citrate and 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→38.63 Å / Num. obs: 51700 / % possible obs: 99.6 % / Redundancy: 12 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.04 / Rsym value: 0.13 / Net I/σ(I): 18.1
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3381 / CC1/2: 0.536 / Rpim(I) all: 0.47 / Rsym value: 1

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.63 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 2660 5.15 %
Rwork0.1685 --
obs0.1703 51678 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6240 0 215 368 6823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036600
X-RAY DIFFRACTIONf_angle_d0.5868975
X-RAY DIFFRACTIONf_dihedral_angle_d5.9421012
X-RAY DIFFRACTIONf_chiral_restr0.0441047
X-RAY DIFFRACTIONf_plane_restr0.0041127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.33781580.28422468X-RAY DIFFRACTION96
2.24-2.280.26611370.25082559X-RAY DIFFRACTION99
2.28-2.330.30171180.23182602X-RAY DIFFRACTION100
2.33-2.380.2285970.22292581X-RAY DIFFRACTION100
2.38-2.430.26251430.21382584X-RAY DIFFRACTION100
2.43-2.490.24751170.212594X-RAY DIFFRACTION100
2.49-2.560.2631460.20642545X-RAY DIFFRACTION99
2.56-2.640.22641380.20172576X-RAY DIFFRACTION100
2.64-2.720.2521580.20332549X-RAY DIFFRACTION100
2.72-2.820.2271150.19482619X-RAY DIFFRACTION100
2.82-2.930.22591700.18572543X-RAY DIFFRACTION100
2.93-3.070.23241400.18592616X-RAY DIFFRACTION100
3.07-3.230.23031600.18272541X-RAY DIFFRACTION99
3.23-3.430.22991200.17062610X-RAY DIFFRACTION100
3.43-3.690.17511300.14812616X-RAY DIFFRACTION100
3.69-4.070.19571580.14192553X-RAY DIFFRACTION100
4.07-4.650.1641080.11862649X-RAY DIFFRACTION100
4.65-5.860.14521990.12692571X-RAY DIFFRACTION100
5.86-38.630.18211480.17062642X-RAY DIFFRACTION98
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)
10.7587-0.08240.12860.83630.13220.56280.031-0.14320.05310.13410.0112-0.0578-0.03680.0656-0.03610.2271-0.0214-0.00380.2434-0.03190.217816.359314.683924.9758
21.9113-0.0809-0.15621.40310.39821.5881-0.0589-0.10270.15710.0140.0393-0.2234-0.19810.2419-0.0260.3093-0.0409-0.04940.3707-0.05750.381736.875517.48925.6542
31.9740.03840.46261.37090.01851.22640.1038-0.0598-0.13740.1394-0.0063-0.32140.02430.2549-0.09470.2352-0.0012-0.04030.313-0.04070.332238.34764.322521.3645
41.6562-0.19070.26871.7532-0.46191.0863-0.00890.0327-0.0114-0.02580.0454-0.0390.01640.0267-0.1120.1732-0.0113-0.00880.2301-0.02840.257923.87821.834416.9052
51.2520.8638-0.67312.9655-0.95122.713-0.2090.2134-0.157-0.48450.0565-0.26140.09990.18520.12270.2877-0.04420.07180.3009-0.08610.324434.095526.0491-8.9629
60.2872-0.0748-0.08162.7337-1.36071.20590.03220.02490.0624-0.2669-0.0101-0.06690.0415-0.00520.00050.2701-0.04530.03110.261-0.07060.333231.200934.336-10.509
71.878-0.16230.8213.1798-1.25243.4268-0.04740.24140.5409-0.4086-0.3432-1.0870.75760.13410.34860.75250.11810.01680.50440.06410.785232.454355.0635-35.7198
81.7196-0.49380.14893.8409-1.70682.90830.0621-0.17160.22420.51060.09070.2573-0.7666-0.0529-0.13010.4454-0.01320.09690.2521-0.02520.316725.515845.2112.23
91.51840.21440.74352.98941.04824.34710.16790.0084-0.0771-0.43610.08430.35930.5961-0.8764-0.24310.6913-0.168-0.11070.52980.12940.470318.62553.5713-26.5329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 267 )
2X-RAY DIFFRACTION2chain 'A' and (resid 268 through 351 )
3X-RAY DIFFRACTION3chain 'A' and (resid 352 through 406 )
4X-RAY DIFFRACTION4chain 'A' and (resid 407 through 468 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 87 )
6X-RAY DIFFRACTION6chain 'H' and (resid 88 through 136 )
7X-RAY DIFFRACTION7chain 'H' and (resid 137 through 231 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 106 )
9X-RAY DIFFRACTION9chain 'L' and (resid 106A through 212 )

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