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- PDB-3u2s: Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV... -

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Basic information

Entry
Database: PDB / ID: 3u2s
TitleCrystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain ZM109
Components
  • Envelope glycoprotein gp120
  • PG9 heavy chain
  • PG9 light chain
KeywordsIMMUNE SYSTEM / greek key / immunoglobulin / immune recognition
Function / homology
Function and homology information


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 ...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
Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Roll / Immunoglobulins ...Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsMcLellan, J.S. / Pancera, M. / Kwong, P.D.
CitationJournal: Nature / Year: 2011
Title: Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, ...Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, Y. / Zhang, B. / Zhou, T. / Zhu, J. / Boyington, J.C. / Chuang, G.Y. / Diwanji, D. / Georgiev, I. / Do Kwon, Y. / Lee, D. / Louder, M.K. / Moquin, S. / Schmidt, S.D. / Yang, Z.Y. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Burton, D.R. / Koff, W.C. / Walker, L.M. / Phogat, S. / Wyatt, R. / Orwenyo, J. / Wang, L.X. / Arthos, J. / Bewley, C.A. / Mascola, J.R. / Nabel, G.J. / Schief, W.R. / Ward, A.B. / Wilson, I.A. / Kwong, P.D.
History
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 3.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 3.3Nov 6, 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: PG9 heavy chain
L: PG9 light chain
G: Envelope glycoprotein gp120
A: PG9 heavy chain
B: PG9 light chain
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,61417
Polymers127,0416
Non-polymers3,57311
Water15,259847
1
H: PG9 heavy chain
L: PG9 light chain
G: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2598
Polymers63,5203
Non-polymers1,7395
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PG9 heavy chain
B: PG9 light chain
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3559
Polymers63,5203
Non-polymers1,8356
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.465, 86.565, 94.879
Angle α, β, γ (deg.)90.00, 92.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules GC

#3: Protein Envelope glycoprotein gp120


Mass: 13489.955 Da / Num. of mol.: 2 / Fragment: V1V2 region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: ZM109 / Gene: env / Plasmid: pVRC8400 / Cell line (production host): HEK293S GnTI / Production host: Homo sapiens (human) / References: UniProt: Q6TCP8*PLUS

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Antibody , 2 types, 4 molecules HALB

#1: Antibody PG9 heavy chain


Mass: 27193.172 Da / Num. of mol.: 2 / Fragment: antigen-binding fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody PG9 light chain


Mass: 22837.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Sugars , 2 types, 4 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]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-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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, 854 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% (w/v) PEG 3350, 5% (v/v) 2-methyl-2,4-pentanediol, 90 mM lithium sulfate, 45 mM imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2011
RadiationMonochromator: Si220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 134186 / Num. obs: 122378 / % possible obs: 91.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2 / Num. unique all: 4342 / % possible all: 64.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: dev_755)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3LRS

3lrs


Resolution: 1.797→41.581 Å / SU ML: 0.5 / σ(F): 0 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 6166 5.04 %random
Rwork0.1779 ---
obs0.1792 122322 90.97 %-
all-134464 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.501 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.5021 Å2-0 Å2-7.885 Å2
2---7.0101 Å20 Å2
3---1.5079 Å2
Refinement stepCycle: LAST / Resolution: 1.797→41.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8082 0 231 847 9160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078522
X-RAY DIFFRACTIONf_angle_d1.0711606
X-RAY DIFFRACTIONf_dihedral_angle_d19.4353078
X-RAY DIFFRACTIONf_chiral_restr0.1021339
X-RAY DIFFRACTIONf_plane_restr0.0041439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7974-1.81780.31721200.27772510X-RAY DIFFRACTION59
1.8178-1.83920.26851510.25092889X-RAY DIFFRACTION68
1.8392-1.86170.26941450.22973008X-RAY DIFFRACTION70
1.8617-1.88520.24261620.21443089X-RAY DIFFRACTION73
1.8852-1.910.21521690.21533210X-RAY DIFFRACTION76
1.91-1.93620.22781760.21763340X-RAY DIFFRACTION79
1.9362-1.96390.21721860.20753485X-RAY DIFFRACTION83
1.9639-1.99320.24452050.20073623X-RAY DIFFRACTION86
1.9932-2.02430.23072080.19433798X-RAY DIFFRACTION89
2.0243-2.05750.23482200.19323898X-RAY DIFFRACTION92
2.0575-2.0930.21912030.18633979X-RAY DIFFRACTION94
2.093-2.1310.2282300.17684023X-RAY DIFFRACTION95
2.131-2.1720.19852260.17064064X-RAY DIFFRACTION96
2.172-2.21640.1882220.16814112X-RAY DIFFRACTION97
2.2164-2.26450.21491840.17284168X-RAY DIFFRACTION97
2.2645-2.31720.20542390.17744092X-RAY DIFFRACTION97
2.3172-2.37520.20662460.16764116X-RAY DIFFRACTION97
2.3752-2.43940.18942090.17484154X-RAY DIFFRACTION98
2.4394-2.51110.20442500.17524133X-RAY DIFFRACTION98
2.5111-2.59220.21192110.18844166X-RAY DIFFRACTION98
2.5922-2.68480.22012380.17424151X-RAY DIFFRACTION98
2.6848-2.79230.19162210.17644212X-RAY DIFFRACTION98
2.7923-2.91930.2022180.17474164X-RAY DIFFRACTION98
2.9193-3.07320.22732070.17964229X-RAY DIFFRACTION98
3.0732-3.26570.21151880.18114218X-RAY DIFFRACTION99
3.2657-3.51770.22332340.18244228X-RAY DIFFRACTION99
3.5177-3.87150.19042310.1714218X-RAY DIFFRACTION99
3.8715-4.43110.17392250.14674269X-RAY DIFFRACTION99
4.4311-5.58060.17172350.15164267X-RAY DIFFRACTION99
5.5806-41.5920.2142070.20364343X-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)
12.9896-1.02760.66182.1265-0.09151.38340.0024-0.1213-0.17380.01390.03180.31990.0261-0.2336-0.03550.1501-0.02150.03180.16740.02110.163127.29651.9461.2314
22.21960.77981.29372.46211.64015.4918-0.0495-0.12920.07340.53010.3225-0.4325-0.01290.5166-0.30410.39160.0958-0.09780.3149-0.10610.344561.24443.472722.224
32.31040.14441.29052.71330.92192.46620.02210.03120.0860.0774-0.02180.0507-0.1113-0.0340.01470.18830.02090.02030.12570.00560.14234.429640.9631.7156
46.9248-2.25220.71917.0208-0.61456.447-0.0486-0.31220.2186-0.1691-0.0563-1.2951-0.08221.02990.10950.50540.0132-0.05330.5176-0.09350.696970.016338.884255.5934
52.43741.63181.63253.68721.39281.9972-0.0673-0.03870.1055-0.0995-0.02380.1663-0.1454-0.04930.06810.15480.0190.03530.15750.00790.137633.735621.91561.7035
66.0173-2.47730.89867.5036-0.05093.4434-0.2110.1257-0.0719-0.05450.2651-0.71520.01450.3895-0.03360.26840.0021-0.01620.3137-0.05630.38566.915814.717311.3162
73.1585-1.38441.55274.5619-0.87031.7150.1149-0.0175-0.240.11120.04630.1470.22260.0459-0.13520.2876-0.0034-0.01150.13590.00910.154937.302121.597138.4678
82.51710.96781.46195.16222.97515.4812-0.009-0.10040.08290.39260.1817-0.4093-0.07330.0712-0.16740.61550.0315-0.10650.3583-0.06780.394657.658629.224462.0787
93.9849-0.59572.42160.8016-0.48311.7755-0.05140.1263-0.2854-0.2786-0.04320.3723-0.05960.1268-0.10430.278-0.0412-0.05720.4987-0.06060.63841.32144.6481-14.7634
102.38611.7851.381.80150.60791.21830.2504-0.58240.31450.4883-0.57760.77010.0821-0.55210.13290.3593-0.1367-0.25090.2638-0.36190.9184-15.655613.4799-15.8558
112.07730.12761.92021.03030.16792.34970.1626-0.0704-0.44870.0763-0.06460.64740.058-0.413-0.08010.32610.0907-0.05070.39740.0090.54866.010638.305318.5872
122.7184-1.20972.22873.05430.78175.07260.82550.8294-0.7984-0.4545-0.4583-0.60731.09150.7715-0.33240.77570.1548-0.220.7551-0.06451.0819-2.15530.0494.6473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain H and resid 1:135
2X-RAY DIFFRACTION2chain H and resid 136:231
3X-RAY DIFFRACTION3chain A and resid 1:135
4X-RAY DIFFRACTION4chain A and resid 136:231
5X-RAY DIFFRACTION5chain L and resid 1:110
6X-RAY DIFFRACTION6chain L and resid 111:210
7X-RAY DIFFRACTION7chain B and resid 1:110
8X-RAY DIFFRACTION8chain B and resid 111:210
9X-RAY DIFFRACTION9chain G and resid 1:195
10X-RAY DIFFRACTION10chain G and resid 196:239
11X-RAY DIFFRACTION11chain C and resid 1:195
12X-RAY DIFFRACTION12chain C and resid 196:250

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