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- PDB-4zyk: Crystal Structure of Quaternary-Specific RSV-Neutralizing Human A... -

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Basic information

Entry
Database: PDB / ID: 4zyk
TitleCrystal Structure of Quaternary-Specific RSV-Neutralizing Human Antibody AM14
Components
  • AM14 Fab heavy chain
  • AM14 light chain
KeywordsIMMUNE SYSTEM / Ig domain / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGilman, M.S.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R43AI112124 United States
CitationJournal: Plos Pathog. / Year: 2015
Title: Characterization of a Prefusion-Specific Antibody That Recognizes a Quaternary, Cleavage-Dependent Epitope on the RSV Fusion Glycoprotein.
Authors: Gilman, M.S. / Moin, S.M. / Mas, V. / Chen, M. / Patel, N.K. / Kramer, K. / Zhu, Q. / Kabeche, S.C. / Kumar, A. / Palomo, C. / Beaumont, T. / Baxa, U. / Ulbrandt, N.D. / Melero, J.A. / ...Authors: Gilman, M.S. / Moin, S.M. / Mas, V. / Chen, M. / Patel, N.K. / Kramer, K. / Zhu, Q. / Kabeche, S.C. / Kumar, A. / Palomo, C. / Beaumont, T. / Baxa, U. / Ulbrandt, N.D. / Melero, J.A. / Graham, B.S. / McLellan, J.S.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 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: AM14 Fab heavy chain
L: AM14 light chain
A: AM14 Fab heavy chain
B: AM14 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,52212
Polymers95,9614
Non-polymers5628
Water11,223623
1
H: AM14 Fab heavy chain
L: AM14 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3597
Polymers47,9802
Non-polymers3785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-37 kcal/mol
Surface area19830 Å2
MethodPISA
2
A: AM14 Fab heavy chain
B: AM14 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1645
Polymers47,9802
Non-polymers1833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-15 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.680, 95.880, 145.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody AM14 Fab heavy chain


Mass: 24365.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody AM14 light chain


Mass: 23615.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 631 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 8.69mg/mL AM14Fab, 0.1M Sodium acetate pH4.5, 0.2M ammonium sulfate, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2→52.582 Å / Num. obs: 66821 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 22.45 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.087 / Net I/σ(I): 6.9 / Num. measured all: 337175 / Scaling rejects: 319
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.054.71.192.22087944290.5420.61599.9
9.38-52.583.90.07611.729737540.990.04199.2

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Processing

Software
NameVersionClassification
Aimless0.3.5data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ERS, 4JHA

4ers

4jha


Resolution: 2→52.582 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 3320 4.98 %Random selection
Rwork0.1861 63405 --
obs0.1881 66725 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112 Å2 / Biso mean: 32.5391 Å2 / Biso min: 5.28 Å2
Refinement stepCycle: final / Resolution: 2→52.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6549 0 34 623 7206
Biso mean--51.1 39.65 -
Num. residues----858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036733
X-RAY DIFFRACTIONf_angle_d0.7569136
X-RAY DIFFRACTIONf_chiral_restr0.0271022
X-RAY DIFFRACTIONf_plane_restr0.0041174
X-RAY DIFFRACTIONf_dihedral_angle_d11.8792414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02860.27941220.2462564268699
2.0286-2.05890.26381300.224226152745100
2.0589-2.09110.25111400.224226072747100
2.0911-2.12530.26721320.216926262758100
2.1253-2.1620.28861370.212526062743100
2.162-2.20130.26151410.216925792720100
2.2013-2.24370.26191320.20926522784100
2.2437-2.28940.26711420.204925912733100
2.2894-2.33920.25261290.209326312760100
2.3392-2.39360.25461460.207426172763100
2.3936-2.45350.26031260.205126262752100
2.4535-2.51980.23461360.202326382774100
2.5198-2.5940.25341430.197926182761100
2.594-2.67770.24981470.199526312778100
2.6777-2.77340.22561170.200826402757100
2.7734-2.88440.23611440.200726392783100
2.8844-3.01570.29491200.196726652785100
3.0157-3.17470.22771360.194426502786100
3.1747-3.37360.21961380.186126422780100
3.3736-3.6340.21531550.165826502805100
3.634-3.99960.18221520.157826672819100
3.9996-4.5780.17261480.140126962844100
4.578-5.76670.16451460.151327172863100
5.7667-52.59990.24251610.194828382999100
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)
13.7227-1.9995-0.0113.9307-0.64084.3942-0.04230.2088-0.2745-0.2999-0.14520.12620.8558-0.59840.16630.4054-0.10490.06750.2494-0.00950.23785.7998-54.678720.085
22.4524-1.2405-1.03352.56350.68382.24810.01720.12710.0948-0.09370.0455-0.10810.04490.0053-0.04930.0682-0.0157-0.00750.10260.00320.09518.0395-34.154-5.1881
31.2063-0.027-0.24761.8552-2.31315.9439-0.0415-0.1157-0.07570.1574-0.0172-0.0462-0.0974-0.17930.05080.17160.00280.00710.16090.04450.15618.751-42.288630.7627
43.7244-0.9413-0.10353.43280.17414.0748-0.1899-0.24840.6229-0.10810.098-0.1577-0.32070.1340.07280.1576-0.0071-0.03710.1748-0.08390.380516.93994.830916.2597
53.9659-1.3559-0.26563.45490.78313.5671-0.0554-0.19350.18020.17230.0385-0.2945-0.1991-0.07790.02040.1835-0.0364-0.05270.1963-0.02090.17834.656-12.73534.4181
63.1364-1.584-0.04653.02610.06062.19570.11910.28480.1893-0.1234-0.12980.1272-0.2525-0.1580.01730.10270.00920.00640.15050.00710.170420.7435-12.71592.6364
71.6142-0.2222-0.55661.23640.0476.1878-0.0169-0.3411-0.14780.3784-0.0599-0.04180.393-0.24890.06310.2466-0.0758-0.04190.2610.05090.208630.2732-28.431635.8225
81.36750.0072-0.08151.3071-0.13280.9882-0.0321-0.0118-0.1998-0.03670.0467-0.03970.27350.0153-0.00250.14790.00150.00970.1028-0.01170.115622.9293-55.6685-6.1276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 123 through 223)A0
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 109)B0
3X-RAY DIFFRACTION3chain 'B' and (resid 110 through 223)B0
4X-RAY DIFFRACTION4chain 'H' and (resid 2 through 122)H0
5X-RAY DIFFRACTION5chain 'H' and (resid 123 through 223)H0
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 110)L0
7X-RAY DIFFRACTION7chain 'L' and (resid 111 through 213)L0
8X-RAY DIFFRACTION8chain 'A' and (resid 2 through 122)A0

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