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- PDB-5igx: Crystal structure of NIH45-46 Fab germline precursor in complex w... -

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Basic information

Entry
Database: PDB / ID: 5igx
TitleCrystal structure of NIH45-46 Fab germline precursor in complex with 426c.TM1deltaV1-3 gp120
Components
  • 426c.TM1deltaV1-3 gp120
  • germline NIH45-46 Fab heavy chain
  • germline NIH45-46 light chain
KeywordsIMMUNE SYSTEM / ANTIBODY / HIV-1
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / 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 / 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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.39 Å
AuthorsScharf, L. / Bjorkman, P.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100148 United States
Bill & Melinda Gates Foundation1040753 United States
American Cancer SocietyPF-13-076-01-MPC United States
CitationJournal: Elife / Year: 2016
Title: Structural basis for germline antibody recognition of HIV-1 immunogens.
Authors: Scharf, L. / West, A.P. / Sievers, S.A. / Chen, C. / Jiang, S. / Gao, H. / Gray, M.D. / McGuire, A.T. / Scheid, J.F. / Nussenzweig, M.C. / Stamatatos, L. / Bjorkman, P.J.
History
DepositionFeb 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list ...pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _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 2.0Jul 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: 426c.TM1deltaV1-3 gp120
H: germline NIH45-46 Fab heavy chain
L: germline NIH45-46 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3957
Polymers88,1453
Non-polymers1,2504
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint2 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.284, 168.533, 176.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein 426c.TM1deltaV1-3 gp120


Mass: 39377.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) / References: UniProt: A0A0K1H6P9*PLUS
#2: Antibody germline NIH45-46 Fab heavy chain


Mass: 25747.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-2936E / Production host: Homo sapiens (human)
#3: Antibody germline NIH45-46 light chain


Mass: 23019.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-2936E / Production host: Homo sapiens (human)
#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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 3
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 22% (w/v) PEG 1,000, 3% (w/v) xylitol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9541 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9541 Å / Relative weight: 1
ReflectionResolution: 3.39→39.17 Å / Num. obs: 15282 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 92.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.034 / Rrim(I) all: 0.125 / Net I/σ(I): 15.8 / Num. measured all: 204811 / Scaling rejects: 557
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.39-3.6613.20.591199.1
8.97-39.1712.70.032199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.17data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JDV

4jdv


Resolution: 3.39→39.167 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 770 5.04 %Random selection
Rwork0.2797 14505 --
obs0.2801 15275 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.59 Å2 / Biso mean: 101.4603 Å2 / Biso min: 48.51 Å2
Refinement stepCycle: final / Resolution: 3.39→39.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 81 0 5085
Biso mean--104.3 --
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085206
X-RAY DIFFRACTIONf_angle_d1.4537157
X-RAY DIFFRACTIONf_chiral_restr0.086865
X-RAY DIFFRACTIONf_plane_restr0.01920
X-RAY DIFFRACTIONf_dihedral_angle_d14.2711726
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3896-3.60190.3281230.32622369249299
3.6019-3.87980.29361220.308723852507100
3.8798-4.26980.28071270.27424012528100
4.2698-4.88660.24281290.25524202549100
4.8866-6.15280.29521300.275124282558100
6.1528-39.16930.29661390.277525022641100
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)
18.93132.3263-0.00561.57210.30011.24980.0762-0.332-1.08070.0562-0.1081-0.55270.15340.6650.15620.53060.04470.03960.641-0.00440.7096-45.417111.25482.3582
22.7210.0138-1.98543.2863-0.88175.0548-0.07140.07490.42010.1403-0.0206-0.6165-0.63990.8122-0.04260.6034-0.21190.0030.6389-0.02060.6979-49.06528.5806-5.0376
32.49811.1901-1.50571.8217-0.673.4064-0.0433-0.1675-0.34350.0722-0.1525-0.5086-0.09450.22120.13180.4775-0.14570.08930.5218-0.00390.7124-52.678621.6428-6.2408
44.1266-0.1622-0.42563.83040.38362.467-0.1151-0.0581-0.1405-0.38910.19090.18110.6511-0.4697-0.07660.9777-0.24180.14110.70680.09660.5871-63.616819.1697-28.4278
53.6642-0.2514-0.21050.248-0.03644.6674-1.1019-0.1377-0.42530.0074-0.0119-0.22340.556-0.61320.5991.4624-0.3116-0.02631.02480.09661.1679-80.108120.4321-55.3103
63.1578-0.983-1.0791.6936-0.9482.2127-0.3450.9387-0.2572-0.91650.2548-0.53560.94720.1822-0.05981.5788-0.32610.40341.23990.08730.8608-47.46517.5197-42.7355
71.3652-0.7626-0.74742.2942-2.11793.41990.15381.8396-0.0685-1.64630.31171.19230.2235-0.5781-0.65912.5383-0.5319-0.06281.81050.55271.1506-67.70628.5372-67.3353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 44 through 215 )G44 - 215
2X-RAY DIFFRACTION2chain 'G' and (resid 216 through 421 )G216 - 421
3X-RAY DIFFRACTION3chain 'G' and (resid 422 through 491 )G422 - 491
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 112 )H1 - 112
5X-RAY DIFFRACTION5chain 'H' and (resid 113 through 211 )H113 - 211
6X-RAY DIFFRACTION6chain 'L' and (resid 1 through 98 )L1 - 98
7X-RAY DIFFRACTION7chain 'L' and (resid 99 through 205 )L99 - 205

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