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- PDB-3u7y: Structure of NIH45-46 Fab in complex with gp120 of 93TH057 HIV -

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Basic information

Entry
Database: PDB / ID: 3u7y
TitleStructure of NIH45-46 Fab in complex with gp120 of 93TH057 HIV
Components
  • Envelope glycoprotein gp160
  • NIH45-46 heavy chain, Ig gamma-1 chain C region
  • NIH45-46 light chain, Ig kappa chain C region
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Ig fold / gp120 / anti HIV / Glycosylation / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / membrane fusion involved in viral entry into host cell / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / membrane fusion involved in viral entry into host cell / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / host cell endosome membrane / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / clathrin-dependent endocytosis of virus by host cell / Potential therapeutics for SARS / adaptive immune response / viral protein processing / immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular space / extracellular exosome / extracellular region / membrane / plasma 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 ...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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / clade A/E 93TH057 HIV-1 gp120 core / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4478 Å
AuthorsDiskin, R. / Bjorkman, P.J.
CitationJournal: Science / Year: 2011
Title: Increasing the Potency and Breadth of an HIV Antibody by Using Structure-Based Rational Design.
Authors: Diskin, R. / Scheid, J.F. / Marcovecchio, P.M. / West, A.P. / Klein, F. / Gao, H. / Gnanapragasam, P.N. / Abadir, A. / Seaman, M.S. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Polymer sequence / Refinement description
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / software / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Nov 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: NIH45-46 heavy chain, Ig gamma-1 chain C region
G: Envelope glycoprotein gp160
L: NIH45-46 light chain, Ig kappa chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,59512
Polymers88,2943
Non-polymers2,3009
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint4 kcal/mol
Surface area34960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.130, 70.500, 217.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules G

#2: Protein Envelope glycoprotein gp160


Mass: 40204.512 Da / Num. of mol.: 1
Fragment: gp120 core (UNP RESIDUES 43-122, 201-303, 325-486)
Mutation: V65C, S115C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Gene: Env, pol / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q0ED31, UniProt: A0A0M3KKW9*PLUS

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Antibody , 2 types, 2 molecules HL

#1: Antibody NIH45-46 heavy chain, Ig gamma-1 chain C region


Mass: 25089.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK 2936E / Production host: Homo sapiens (human) / References: UniProt: P01857
#3: Antibody NIH45-46 light chain, Ig kappa chain C region


Mass: 23000.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Cell line (production host): HEK 2936E / Production host: Homo sapiens (human) / References: UniProt: P01834

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Sugars , 2 types, 7 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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.: 6
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 , 3 types, 69 molecules

#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12% isopropanol, 10% polyethylene glycol 10,000, 0.1 M sodium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2011
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4478→37.05 Å / Num. all: 39608 / Num. obs: 39062 / % possible obs: 98.6 %
Reflection shellResolution: 2.4478→2.51 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_805)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U7W AND 3NGB

3u7w

3ngb


Resolution: 2.4478→37.05 Å / SU ML: 0.94 / σ(F): 1.34 / Phase error: 32.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 2112 5.42 %5.5%
Rwork0.2068 ---
obs0.2095 38987 97.1 %-
all-39608 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.203 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.9262 Å20 Å2-0 Å2
2--5.4197 Å20 Å2
3----18.346 Å2
Refinement stepCycle: LAST / Resolution: 2.4478→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 148 67 6193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046299
X-RAY DIFFRACTIONf_angle_d0.7548549
X-RAY DIFFRACTIONf_dihedral_angle_d16.2922273
X-RAY DIFFRACTIONf_chiral_restr0.051962
X-RAY DIFFRACTIONf_plane_restr0.0031091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4478-2.50480.4151120.36311949X-RAY DIFFRACTION78
2.5048-2.56740.41171460.37822434X-RAY DIFFRACTION98
2.5674-2.63680.39591390.33292439X-RAY DIFFRACTION98
2.6368-2.71440.39971370.3192471X-RAY DIFFRACTION98
2.7144-2.80190.36731360.29612429X-RAY DIFFRACTION98
2.8019-2.90210.35461400.27082480X-RAY DIFFRACTION99
2.9021-3.01820.31861470.24652459X-RAY DIFFRACTION99
3.0182-3.15550.31961460.24322486X-RAY DIFFRACTION99
3.1555-3.32180.29421410.24392502X-RAY DIFFRACTION99
3.3218-3.52970.26961290.22662464X-RAY DIFFRACTION97
3.5297-3.8020.26911470.20492495X-RAY DIFFRACTION99
3.802-4.18410.22631390.1742526X-RAY DIFFRACTION99
4.1841-4.78850.18591470.14052496X-RAY DIFFRACTION98
4.7885-6.02880.18981510.16282578X-RAY DIFFRACTION99
6.0288-37.05390.24711550.20562667X-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)
13.47480.3594-0.11153.27970.19425.9784-0.00950.0005-0.03130.2006-0.24680.2097-0.1425-0.43730.26250.5595-0.04480.03370.3108-0.06790.2368-4.8932-26.2415-28.1055
25.08180.3862-1.94475.72821.74046.976-0.234-0.01720.006-0.05620.29440.52910.2443-1.0257-0.05380.5048-0.04350.03110.5880.14880.5114-25.2451-45.332-1.0862
33.71081.48421.2054.88523.35992.40280.08830.00640.16690.3601-0.20360.0450.81010.83530.15920.639-0.04330.05170.57540.11450.450310.1185.1187-52.2695
45.00722.84922.85365.7013-0.01446.08920.1667-0.17430.18950.5909-0.3202-0.3264-0.57740.43310.06270.7061-0.01940.1110.45030.09430.390213.74521.9892-43.3423
51.30951.294-0.07764.2094-0.76064.4762-0.17890.11130.35650.3151-0.2742-0.1283-0.94070.60030.30570.45010.08760.01470.30910.13170.324610.4997-3.6873-47.798
62.7818-0.4389-1.41294.4909-0.61085.05610.09970.3146-0.048-0.2935-0.3222-0.68340.14450.69110.18060.33510.12160.0880.65710.20860.514319.6258-20.4307-46.1101
76.3308-1.52513.5834.9286-2.53275.141-0.1326-0.29750.2868-0.254-0.3921-0.45350.49860.48340.5310.64570.17330.09610.47230.06420.447910.9223-25.1703-47.3345
80.88571.0492-0.39831.3279-0.24391.258-0.22760.9236-0.816-0.514-0.3374-0.5040.96820.81690.26790.95570.30640.26660.79480.10460.53313.041-28.695-53.24
92.81540.81450.30291.540.47983.52950.08310.77750.5764-0.7049-0.30410.00450.3758-0.06270.2350.54890.0804-0.01670.58340.12070.38196.0724-17.704-54.3821
103.6972-4.2193-5.26895.17286.27887.7077-0.4166-0.08950.907-0.1749-0.6445-1.14531.7171.13050.79380.6317-0.020.00220.69420.09210.677413.3528-27.7233-31.7243
114.58433.47732.95426.80494.55926.49770.5921-0.5905-0.49891.1326-0.8184-0.9418-0.2777-0.06150.33750.7958-0.0966-0.07340.5240.20350.404913.9789-1.037-39.5534
128.9454-1.683-5.75842.83382.04586.519-0.3129-1.1254-0.21550.8670.00910.01170.10591.0350.14011.2798-0.2308-0.03570.61740.06460.41493.1918-22.9971-1.5575
135.6569-2.37325.05135.63250.32547.4135-0.3425-0.15020.9130.39180.0427-0.3153-0.5363-0.41090.10310.9619-0.27090.12380.4398-0.08170.283-0.595-19.5912-12.8393
145.3321-2.45560.11191.72920.17998.5651-0.3548-1.03360.73681.27260.0074-0.2597-0.75680.12480.15861.2307-0.26610.02150.478-0.09550.56763.7669-12.1999-7.5302
150.7623-0.4735-0.35270.4912-1.34461.76410.2515-0.31670.05290.6698-0.20920.1251-0.73820.1103-0.22040.9288-0.16650.1040.4803-0.05450.2209-8.4619-33.1915-0.6015
162.7178-0.615-0.60147.44426.22748.57620.0356-0.6494-0.1707-0.28520.0811-0.8287-0.44360.5353-0.01620.6075-0.08880.11190.68380.13460.4528-10.2605-45.21758.737
172.7339-0.5107-1.91595.98874.17035.04050.16-0.2717-0.1584-0.4934-0.237-0.4404-0.27820.15460.02710.6255-0.01850.03620.49840.13180.4387-11.3367-48.29554.5487
184.42182.52953.34219.59545.21289.50770.3021-1.1367-0.77960.6253-0.2705-0.30750.0164-0.70830.09960.72880.11220.07750.89520.20290.6949-11.0494-53.469914.5256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resseq 2:115)
2X-RAY DIFFRACTION2chain 'H' and (resseq 116:218)
3X-RAY DIFFRACTION3chain 'G' and (resseq 44:73)
4X-RAY DIFFRACTION4chain 'G' and (resseq 74:115)
5X-RAY DIFFRACTION5chain 'G' and (resseq 116:258)
6X-RAY DIFFRACTION6chain 'G' and (resseq 259:353)
7X-RAY DIFFRACTION7chain 'G' and (resseq 354:392)
8X-RAY DIFFRACTION8chain 'G' and (resseq 393:425)
9X-RAY DIFFRACTION9chain 'G' and (resseq 426:456)
10X-RAY DIFFRACTION10chain 'G' and (resseq 457:474)
11X-RAY DIFFRACTION11chain 'G' and (resseq 475:492)
12X-RAY DIFFRACTION12chain 'L' and (resseq 3:24)
13X-RAY DIFFRACTION13chain 'L' and (resseq 25:46)
14X-RAY DIFFRACTION14chain 'L' and (resseq 47:73)
15X-RAY DIFFRACTION15chain 'L' and (resseq 74:124)
16X-RAY DIFFRACTION16chain 'L' and (resseq 125:146)
17X-RAY DIFFRACTION17chain 'L' and (resseq 147:184)
18X-RAY DIFFRACTION18chain 'L' and (resseq 185:210)

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