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- PDB-5uem: Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE s... -

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Entry
Database: PDB / ID: 5uem
TitleCrystal structure of 354NC37 Fab in complex with HIV-1 clade AE strain 93TH057 gp120
Components
  • 354NC37 Fab Heavy Chain
  • 354NC37 Fab Light Chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM / HIV / Envelope Protein / Antibody / Immunity
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSievers, S.A. / Gristick, H.B. / Bjorkman, P.J.
CitationJournal: Sci Transl Med / Year: 2017
Title: Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller.
Authors: Freund, N.T. / Wang, H. / Scharf, L. / Nogueira, L. / Horwitz, J.A. / Bar-On, Y. / Golijanin, J. / Sievers, S.A. / Sok, D. / Cai, H. / Cesar Lorenzi, J.C. / Halper-Stromberg, A. / Toth, I. / ...Authors: Freund, N.T. / Wang, H. / Scharf, L. / Nogueira, L. / Horwitz, J.A. / Bar-On, Y. / Golijanin, J. / Sievers, S.A. / Sok, D. / Cai, H. / Cesar Lorenzi, J.C. / Halper-Stromberg, A. / Toth, I. / Piechocka-Trocha, A. / Gristick, H.B. / van Gils, M.J. / Sanders, R.W. / Wang, L.X. / Seaman, M.S. / Burton, D.R. / Gazumyan, A. / Walker, B.D. / West, A.P. / Bjorkman, P.J. / Nussenzweig, M.C.
History
DepositionJan 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 2.1Oct 4, 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

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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
H: 354NC37 Fab Heavy Chain
L: 354NC37 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,20913
Polymers88,0733
Non-polymers4,13610
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint44 kcal/mol
Surface area34740 Å2
Unit cell
Length a, b, c (Å)63.635, 67.507, 210.664
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

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


Mass: 40204.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9

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Antibody , 2 types, 2 molecules HL

#2: Antibody 354NC37 Fab Heavy Chain


Mass: 24704.816 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 354NC37 Fab Light Chain


Mass: 23163.916 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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Sugars , 4 types, 9 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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.: 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 , 2 types, 71 molecules

#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20% (w/v) PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→35.743 Å / Num. obs: 27104 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.4
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.83 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7Y

3u7y


Resolution: 2.7→35.743 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 1431 5.57 %
Rwork0.2198 --
obs0.2223 25671 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→35.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 271 70 6296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026399
X-RAY DIFFRACTIONf_angle_d0.618754
X-RAY DIFFRACTIONf_dihedral_angle_d12.2073792
X-RAY DIFFRACTIONf_chiral_restr0.044969
X-RAY DIFFRACTIONf_plane_restr0.0041096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.79650.34421360.29142363X-RAY DIFFRACTION100
2.7965-2.90840.30841340.29032398X-RAY DIFFRACTION100
2.9084-3.04070.30461380.27292391X-RAY DIFFRACTION100
3.0407-3.20090.25791520.26192401X-RAY DIFFRACTION100
3.2009-3.40130.29641350.23242383X-RAY DIFFRACTION100
3.4013-3.66370.28611500.22132378X-RAY DIFFRACTION100
3.6637-4.03190.2761480.20052445X-RAY DIFFRACTION100
4.0319-4.61430.22381400.17532431X-RAY DIFFRACTION100
4.6143-5.80950.22071440.18692478X-RAY DIFFRACTION100
5.8095-35.74570.26391540.2222572X-RAY DIFFRACTION99
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)
12.0736-0.3578-0.15051.62540.271.6638-0.1829-0.1517-0.24530.04530.08490.37860.4039-0.3810.14970.3652-0.0650.02470.33290.00180.327916.7178-31.3977-43.2393
20.66220.5268-0.51112.1411-0.3591.4305-0.149-0.0066-0.0755-0.1530.06550.07530.198-0.05540.00310.20540.0225-0.00980.2626-0.02460.198519.591-19.8237-42.184
32.5831-0.69640.83950.68070.82552.4086-0.10450.24960.2741-0.16310.03920.2825-0.4557-0.73260.12920.35020.0707-0.06680.2808-0.03250.378211.3505-1.4853-48.0844
40.94530.5101-0.48311.4574-0.5831.1717-0.09920.040.0984-0.1041-0.00250.1585-0.0682-0.19110.12220.2650.0639-0.05490.269-0.05870.244619.9552-5.7486-43.1139
53.02670.9334-0.15452.8920.36563.55630.07930.10710.2310.0346-0.2229-0.0622-0.3477-0.07520.1570.23090.0224-0.0150.19160.01910.164241.1146-1.0672-28.9899
62.68971.63131.86141.58771.80942.5240.14930.0160.09330.1395-0.083-0.0750.24090.07560.00860.28430.02120.02280.24010.03970.286149.1918-1.3351-15.1442
73.16511.3042-1.42813.7244-0.93013.95870.1668-0.0232-0.0167-0.13620.1549-0.0106-0.06330.3121-0.25920.2801-0.0384-0.06770.19940.01270.479666.34048.0321-4.1062
83.7088-0.12722.81142.62750.00443.8191-0.3138-0.5799-0.08370.47820.07920.4453-0.2164-0.81070.11150.3164-0.06220.06390.5005-0.00010.238234.0706-12.6561-4.8497
91.4130.5969-1.5083.0426-1.02252.8335-0.111-0.3744-0.1817-0.1564-0.2578-0.248-0.01840.21640.20920.3025-0.045-0.01080.24980.01220.140741.5748-13.4887-15.1101
107.41110.4320.28071.3941-1.33243.4768-0.039-0.0111-0.8746-0.3796-0.1514-0.11050.92860.28660.29390.412-0.02560.04970.1392-0.00230.265940.9014-23.4062-14.2102
111.6901-0.07581.45881.95990.39732.05950.099-0.1423-0.25870.2870.10550.05150.4447-0.4313-0.22780.3091-0.09430.05470.310.00620.212738.8714-16.7659-7.8904
120.55861.0878-0.14032.18620.05670.6501-0.1045-0.59850.03770.3933-0.1203-0.1234-0.1637-0.69760.33960.16660.05930.0560.2656-0.0140.23242.9255-6.8247-2.2983
131.9454-0.3854-0.7621.68141.23762.26220.327-0.10810.4917-0.0187-0.0378-0.302-0.3742-0.027-0.2870.27740.0199-0.03570.2929-0.00530.528554.814911.85666.5429
141.2677-1.2424-0.06932.2462-0.59250.69050.2802-0.4085-0.0695-0.5772-0.09680.5042-0.15970.2461-0.13530.2946-0.0379-0.01720.43070.12530.518448.684410.55851.8571
152.40450.63620.9958.4928-0.32325.99120.3087-0.2701-0.30550.2305-0.1243-0.86131.14370.4587-0.45770.3197-0.0202-0.22440.2546-0.00940.184855.8997-5.61723.1908
163.75220.77340.08597.00441.48961.76470.1976-0.01580.75460.4227-0.1291-0.1606-0.3194-0.1207-0.12520.28190.03790.00210.3007-0.03570.450152.480315.695110.8753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 44 through 98 )
2X-RAY DIFFRACTION2chain 'G' and (resid 99 through 291 )
3X-RAY DIFFRACTION3chain 'G' and (resid 292 through 352 )
4X-RAY DIFFRACTION4chain 'G' and (resid 353 through 491 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 84 )
6X-RAY DIFFRACTION6chain 'H' and (resid 85 through 140 )
7X-RAY DIFFRACTION7chain 'H' and (resid 141 through 214 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 30 )
9X-RAY DIFFRACTION9chain 'L' and (resid 31 through 49 )
10X-RAY DIFFRACTION10chain 'L' and (resid 50 through 62 )
11X-RAY DIFFRACTION11chain 'L' and (resid 63 through 91 )
12X-RAY DIFFRACTION12chain 'L' and (resid 92 through 115 )
13X-RAY DIFFRACTION13chain 'L' and (resid 116 through 152 )
14X-RAY DIFFRACTION14chain 'L' and (resid 153 through 165 )
15X-RAY DIFFRACTION15chain 'L' and (resid 166 through 176 )
16X-RAY DIFFRACTION16chain 'L' and (resid 177 through 211 )

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