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- PDB-5w4l: Crystal structure of the non-neutralizing and ADCC-potent C11-lik... -

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Entry
Database: PDB / ID: 5w4l
TitleCrystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.
Components
  • (Antibody N12-i3 ...) x 2
  • (Antibody N5-i5 ...) x 2
  • CD4 mimetic peptide M48U1
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 gp120 / Clade A/E 93TH057 / Viral protein / Viral protein-immune system complex
Function / homology
Function and homology information


Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CD4-MIMETIC MINIPROTEIN M48U1 / clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsTolbert, W.D. / Gohain, N. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI116274 United States
CitationJournal: Structure / Year: 2017
Title: Targeting the Late Stage of HIV-1 Entry for Antibody-Dependent Cellular Cytotoxicity: Structural Basis for Env Epitopes in the C11 Region.
Authors: Tolbert, W.D. / Gohain, N. / Alsahafi, N. / Van, V. / Orlandi, C. / Ding, S. / Martin, L. / Finzi, A. / Lewis, G.K. / Ray, K. / Pazgier, M.
History
DepositionJun 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_assembly_gen
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3May 30, 2018Group: Data collection / Structure summary / Category: pdbx_entry_details / pdbx_molecule_features / Item: _pdbx_entry_details.compound_details
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
N: CD4 mimetic peptide M48U1
H: Antibody N5-i5 Fab heavy chain
L: Antibody N5-i5 light chain
D: Antibody N12-i3 Fab heavy chain
E: Antibody N12-i3 light chain
A: clade A/E 93TH057 HIV-1 gp120 core
M: CD4 mimetic peptide M48U1
F: Antibody N5-i5 Fab heavy chain
I: Antibody N5-i5 light chain
B: Antibody N12-i3 Fab heavy chain
C: Antibody N12-i3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,30135
Polymers280,58512
Non-polymers4,71623
Water36020
1
G: clade A/E 93TH057 HIV-1 gp120 core
N: CD4 mimetic peptide M48U1
H: Antibody N5-i5 Fab heavy chain
L: Antibody N5-i5 light chain
D: Antibody N12-i3 Fab heavy chain
E: Antibody N12-i3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,76118
Polymers140,2926
Non-polymers2,46912
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: clade A/E 93TH057 HIV-1 gp120 core
M: CD4 mimetic peptide M48U1
F: Antibody N5-i5 Fab heavy chain
I: Antibody N5-i5 light chain
B: Antibody N12-i3 Fab heavy chain
C: Antibody N12-i3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,54017
Polymers140,2926
Non-polymers2,24811
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)311.018, 53.291, 223.577
Angle α, β, γ (deg.)90.00, 128.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 4 types, 8 molecules HFLIDBEC

#3: Antibody Antibody N5-i5 Fab heavy chain


Mass: 23789.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#4: Antibody Antibody N5-i5 light chain


Mass: 22943.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#5: Antibody Antibody N12-i3 Fab heavy chain


Mass: 24170.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#6: Antibody Antibody N12-i3 light chain


Mass: 23485.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Protein / Protein/peptide / Sugars , 3 types, 25 molecules GANM

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 42847.676 Da / Num. of mol.: 2 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell line (production host): GnT1- 293 / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#2: Protein/peptide CD4 mimetic peptide M48U1


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: CD4-MIMETIC MINIPROTEIN M48U1
#7: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
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, 22 molecules

#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD, FOLLOWED BY MANY ROUNDS OF ITERATIVE OPTIMIZATION
Sequence detailsAuthor states that the reference sequence from the database represents a truncated version of the ...Author states that the reference sequence from the database represents a truncated version of the full length HIV Env sequence. Numbering of the gp120 is based on the Hxbc2 Env. Chains G and A both have a histidine to serine mutation at position 375 in the structure. Residues 31-43 and 493-511 are the full length N and C-termini of the sequence referenced in the database.

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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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% PEG 2000 MME 0.1 M Tris-HCl pH 8.0 0.1 M KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 27, 2015 / Details: Rh coated flat bent mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 62153 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 6
Reflection shellResolution: 2.92→3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H8W

4h8w


Resolution: 2.92→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.854 / SU B: 70.063 / SU ML: 0.574 / Cross valid method: THROUGHOUT / ESU R Free: 0.496 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29191 3079 5 %RANDOM
Rwork0.23132 ---
obs0.23426 59072 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.88 Å2
2---1.9 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18756 0 296 20 19072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01919575
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217495
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.96526623
X-RAY DIFFRACTIONr_angle_other_deg0.97340894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09552439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49724.573772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51153097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8561580
X-RAY DIFFRACTIONr_chiral_restr0.0730.23041
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02121480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023767
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4933.1049848
X-RAY DIFFRACTIONr_mcbond_other0.4933.1049847
X-RAY DIFFRACTIONr_mcangle_it0.8754.64612247
X-RAY DIFFRACTIONr_mcangle_other0.8754.64612248
X-RAY DIFFRACTIONr_scbond_it0.7323.2339726
X-RAY DIFFRACTIONr_scbond_other0.7323.2339727
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3454.83114376
X-RAY DIFFRACTIONr_long_range_B_refined3.8659.34276894
X-RAY DIFFRACTIONr_long_range_B_other3.8659.34176895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.921→2.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 206 -
Rwork0.359 3589 -
obs--82.37 %
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)
12.4827-0.2817-0.87162.68390.81452.2346-0.1371-0.36040.24090.41070.149-0.14370.03680.1203-0.01190.12760.05-0.1170.0603-0.05410.2134-30.7614-9.993968.8756
21.9394-0.36140.52083.0989-1.42882.1231-0.0419-0.2646-0.20130.29820.1590.4886-0.0386-0.2316-0.11710.06570.02970.02350.06470.00850.5112-78.2667-38.108657.6641
31.6493-1.1295-1.04453.06291.15863.5596-0.14670.15820.0428-0.63660.0636-0.0692-0.0030.18920.08310.2508-0.06510.00710.0520.00240.176-31.43-26.420435.2494
41.26120.4551-0.02224.08252.59645.24860.12480.5524-0.3516-0.6583-0.48790.8353-0.488-1.03910.36310.99130.01750.03770.8832-0.16050.8516-28.0862-47.70053.2294
52.3576-1.01210.01993.2749-1.06044.02130.07980.62840.0688-0.8337-0.1545-0.1196-0.0632-0.13910.07470.29360.0088-0.05450.17920.00150.4023-62.571-21.38528.0565
60.5272-0.28041.01410.2159-0.56281.9617-0.27270.43660.11490.2053-0.0726-0.2979-0.54460.82640.34541.7282-0.0524-0.00031.43040.18771.5224-56.95132.5796-2.2682
70.82490.82690.50366.27021.29763.187-0.07220.151-0.0768-0.00280.1599-0.07430.30490.1428-0.08760.06890.00910.03270.04130.01280.2575-29.7393-46.185344.1112
80.7594-1.0586-0.61912.58730.2426.3308-0.19520.0741-0.191-0.317-0.1966-0.47730.37850.81650.39180.9276-0.04460.15460.5611-0.00070.7081-15.6375-54.38512.5959
91.6685-0.2693-1.22234.37510.37012.34830.2150.09180.585-0.51110.1540.0456-0.48280.1611-0.3690.27070.04020.01710.12090.06920.6362-67.7897-1.781835.7415
102.53410.55162.74480.40911.47146.3856-0.3320.09380.1691-0.25630.18250.1008-0.947-0.13320.14961.2936-0.0355-0.13210.79430.08020.9012-71.23366.71984.4987
115.7084-3.30130.95333.5802-0.23750.64990.01280.2052-0.41640.0438-0.09480.2680.21210.07250.0820.25280.0584-0.05970.2105-0.0150.201314.2437-48.342458.4607
122.6504-1.74010.3293.5785-0.69960.77790.33760.47250.4254-0.3635-0.344-0.2758-0.28070.03040.00650.30930.1011-0.00740.41790.11850.5046-112.35951.637428.5618
134.1034-1.41420.89331.8631-0.1731.7172-0.4532-1.20340.06920.53210.38420.1413-0.0991-0.22420.0690.47690.1549-0.13760.38520.03530.321322.014-45.074474.6769
142.2481-1.98790.2043.7756-1.46661.0493-0.00950.14340.0874-0.00150.22150.2467-0.1983-0.2735-0.2120.21950.0992-0.07330.32720.05420.4729-126.4522-0.827639.7381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1G31 - 492
2X-RAY DIFFRACTION2A32 - 492
3X-RAY DIFFRACTION3H1 - 113
4X-RAY DIFFRACTION4H114 - 213
5X-RAY DIFFRACTION5F1 - 113
6X-RAY DIFFRACTION6F114 - 213
7X-RAY DIFFRACTION7L3 - 107
8X-RAY DIFFRACTION8L108 - 209
9X-RAY DIFFRACTION9I3 - 107
10X-RAY DIFFRACTION10I108 - 209
11X-RAY DIFFRACTION11D1 - 212
12X-RAY DIFFRACTION12B1 - 212
13X-RAY DIFFRACTION13E2 - 213
14X-RAY DIFFRACTION14C1 - 211

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