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- PDB-4dvr: Crystal structure of YU2 gp120 core in complex with Fab 48d and N... -

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Basic information

Entry
Database: PDB / ID: 4dvr
TitleCrystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557
Components
  • Envelope glycoprotein gp120
  • Fab 48d Heavy chain
  • Fab 48d Light chain
KeywordsIMMUNE SYSTEM/TRANSCRIPTION INHIBITOR / HIV-1 gp120 / CD4 binding site / NBD-557 / IMMUNE SYSTEM-TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / 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 / virion membrane / structural molecule activity / membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-0LY / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: Plos One / Year: 2014
Title: Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site.
Authors: Kwon, Y.D. / Lalonde, J.M. / Yang, Y. / Elban, M.A. / Sugawara, A. / Courter, J.R. / Jones, D.M. / Smith, A.B. / Debnath, A.K. / Kwong, P.D.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Non-polymer description
Revision 1.3May 31, 2017Group: Structure summary
Revision 1.4Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 19, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.6Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Envelope glycoprotein gp120
L: Fab 48d Light chain
H: Fab 48d Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,32811
Polymers81,3973
Non-polymers1,9318
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-4 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.445, 109.738, 130.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer

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Components

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Antibody , 2 types, 2 molecules LH

#2: Antibody Fab 48d Light chain


Mass: 23092.562 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 Fab 48d Heavy chain


Mass: 23386.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 8 molecules G

#1: Protein Envelope glycoprotein gp120 / Env polyprotein


Mass: 34918.633 Da / Num. of mol.: 1 / Fragment: unp residues 82-122; 199-297; 319-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)
Strain: isolate YU-2 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P35961
#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.: 7
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, 114 molecules

#5: Chemical ChemComp-0LY / N-(4-bromophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide / NBD-557


Mass: 382.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24BrN3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CRYSTALLIZED SEQUENCE WAS CONSTRUCTED BY DELETION OF N-TERMINAL 1-43, BY REPLACING THE V1/V2 ...THE CRYSTALLIZED SEQUENCE WAS CONSTRUCTED BY DELETION OF N-TERMINAL 1-43, BY REPLACING THE V1/V2 REGIONS WITH A GG LINKER, AND REPLACING V3 REGION WITH A LINKER GGSGSG

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 5% iso-propanol, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.4 Å / Num. all: 27379 / Num. obs: 24559 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.155 / Net I/σ(I): 11.04
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.46 / % possible all: 62.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1RZK

1rzk


Resolution: 2.5→49.4 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.46 / σ(F): 1.42 / Phase error: 35.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2887 1970 8.16 %
Rwork0.2284 --
obs0.2333 24129 87.79 %
all-27496 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.8165 Å2
Baniso -1Baniso -2Baniso -3
1-2.8745 Å20 Å20 Å2
2---0.3003 Å2-0 Å2
3----2.5742 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5533 0 121 113 5767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0015792
X-RAY DIFFRACTIONf_angle_d0.3597862
X-RAY DIFFRACTIONf_dihedral_angle_d7.0272116
X-RAY DIFFRACTIONf_chiral_restr0.022895
X-RAY DIFFRACTIONf_plane_restr0.002998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4966-2.55910.4201900.32741009X-RAY DIFFRACTION56
2.5591-2.62830.41251000.31451163X-RAY DIFFRACTION66
2.6283-2.70560.35811130.32171264X-RAY DIFFRACTION72
2.7056-2.79290.41881220.30841363X-RAY DIFFRACTION76
2.7929-2.89270.40861330.3061482X-RAY DIFFRACTION84
2.8927-3.00850.40871410.29471576X-RAY DIFFRACTION88
3.0085-3.14540.35151510.29281691X-RAY DIFFRACTION94
3.1454-3.31120.30361530.26341721X-RAY DIFFRACTION97
3.3112-3.51860.33661560.24441758X-RAY DIFFRACTION99
3.5186-3.79020.25841590.23371793X-RAY DIFFRACTION99
3.7902-4.17150.29261600.20981793X-RAY DIFFRACTION99
4.1715-4.77470.23021590.18351803X-RAY DIFFRACTION99
4.7747-6.01390.24461640.19571833X-RAY DIFFRACTION99
6.0139-49.47760.26511690.21171910X-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)
14.3939-3.25482.30386.6073-1.52383.67970.1752-0.0979-0.0567-0.0924-0.0224-0.42380.1660.3224-0.13920.439-0.02780.00390.489-0.11110.368643.46676.010187.9153
23.9122-1.38590.45383.8768-0.20433.6564-0.0349-0.27950.13580.32440.225-0.471-0.16530.1099-0.19960.4549-0.05040.01620.3299-0.03210.389341.943821.607100.7025
34.4743-0.41952.29377.7229-2.80664.9214-0.3318-0.0699-0.00450.74120.44130.0364-0.1766-0.0215-0.11190.47370.04770.01580.49310.02910.352423.297445.848680.9719
47.1487-0.10642.17274.3729-0.69923.6958-0.1638-0.50530.22420.10040.04050.2325-0.7514-0.81820.18470.67290.12940.01540.66930.01020.37422.512169.087965.1466
51.7299-0.76621.96640.3289-0.83762.16750.0586-0.4352-1.01380.18360.6611.00920.1456-0.65-0.43830.4198-0.1262-0.0510.67470.39240.92833.987534.78176.4624
65.36032.8943-0.37628.124-3.10845.20990.1881-0.1572-0.0655-0.2347-0.01510.5624-0.7008-0.2828-0.19460.53350.12570.08240.4290.04110.409-0.181660.984751.7526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G and (resid 1:252 or resid 474:492)
2X-RAY DIFFRACTION2chain G and resid 253:473
3X-RAY DIFFRACTION3chain H and resid 1:118
4X-RAY DIFFRACTION4chain H and resid 119:219
5X-RAY DIFFRACTION5chain L and resid 1:108
6X-RAY DIFFRACTION6chain L and resid 109:212

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