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- PDB-3mnw: Crystal structure of the non-neutralizing HIV antibody 13H11 Fab ... -

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Basic information

Entry
Database: PDB / ID: 3mnw
TitleCrystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41 MPER-derived peptide in a helical conformation
Components
  • ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
  • ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
  • Gp41
KeywordsIMMUNE SYSTEM / HIV-1 / HIV gp41 / MPER / 13H11 / 2F5 / Z13 / 4E10 / Fab antibody
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / immunoglobulin complex / Binding and entry of HIV virion / 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 ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / immunoglobulin complex / Binding and entry of HIV virion / 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 / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 / extracellular region / membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Ig-like domain-containing protein / IgG H chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNicely, N.I. / Dennison, S.M. / Kelsoe, G. / Liao, H.-X. / Alam, S.M. / Haynes, B.F.
CitationJournal: To be Published
Title: Crystal Structure of a Non-Neutralizing HIV-1 gp41 Envelope Antibody Demonstrates Neutralization Mechanism of gp41 Antibodies
Authors: Nicely, N.I. / Dennison, S.M. / Kelsoe, G. / Ueda, Y. / Liao, H.X. / Alam, S.M. / Haynes, B.F.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _pdbx_entity_src_syn.pdbx_beg_seq_num ..._entity.pdbx_fragment / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Gp41
A: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
B: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8054
Polymers50,7433
Non-polymers621
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: Gp41
A: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
B: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
hetero molecules

P: Gp41
A: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
B: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6108
Polymers101,4856
Non-polymers1242
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area10640 Å2
ΔGint-66 kcal/mol
Surface area39230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.753, 160.989, 141.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein/peptide Gp41 /


Mass: 2501.724 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: chemically synthesized peptide of sequence derived from the membrane proximal external region of gp41
Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#2: Antibody ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN


Mass: 24719.545 Da / Num. of mol.: 1 / Fragment: mouse Fv,human Fc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#3: Antibody ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN


Mass: 23521.475 Da / Num. of mol.: 1 / Fragment: mouse Fv,human Fc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Cell line (production host): HEK293T CELL / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: S6B291
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.2
Details: Reservoir: Qiagen Classics II screen H10 (0.2 M K Na tartrate, 20% PEG 3350). Drop: 0.6 uL protein + 0.4 uL reservoir., pH 7.2, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→47 Å / Num. all: 25866 / Num. obs: 24443 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: dev_271)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MNV

3mnv


Resolution: 2.2→40.6 Å / SU ML: 0.33 / σ(F): 0.13 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1986 8.19 %
Rwork0.1811 --
obs0.1869 24245 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.952 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7826 Å20 Å20 Å2
2--0.2254 Å2-0 Å2
3---2.5573 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 4 272 3685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093525
X-RAY DIFFRACTIONf_angle_d1.1174786
X-RAY DIFFRACTIONf_dihedral_angle_d16.7441243
X-RAY DIFFRACTIONf_chiral_restr0.07534
X-RAY DIFFRACTIONf_plane_restr0.012606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.27871440.20881614X-RAY DIFFRACTION97
2.255-2.3160.32681410.21121617X-RAY DIFFRACTION96
2.316-2.38410.31581450.21581604X-RAY DIFFRACTION96
2.3841-2.46110.29511460.20921612X-RAY DIFFRACTION96
2.4611-2.5490.30921400.20451570X-RAY DIFFRACTION94
2.549-2.65110.26511380.19381559X-RAY DIFFRACTION94
2.6511-2.77170.2671420.18561571X-RAY DIFFRACTION93
2.7717-2.91780.24531410.18091571X-RAY DIFFRACTION93
2.9178-3.10050.25511380.17891541X-RAY DIFFRACTION91
3.1005-3.33980.27421380.17991551X-RAY DIFFRACTION91
3.3398-3.67570.24621380.16761549X-RAY DIFFRACTION91
3.6757-4.20710.22121380.16131558X-RAY DIFFRACTION91
4.2071-5.29870.20971430.12731631X-RAY DIFFRACTION94
5.2987-40.60650.20171540.17991711X-RAY DIFFRACTION93
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)
12.95092.5796-2.83118.4988-4.41353.03560.4647-0.41880.4830.7705-0.28220.6938-0.65220.4817-0.20820.1820.04850.00740.214-0.01020.1845-31.3641-18.2377-6.1504
23.5252-0.31852.02630.1283-0.70525.46260.2857-0.2672-0.68710.22410.14990.17590.4448-0.1605-0.30430.1819-0.0427-0.00440.20410.02350.2147-34.3417-29.5824-5.4506
33.3011.281-1.35680.8103-0.00311.3393-0.20140.72380.7761-0.08590.00730.2619-0.1387-0.42960.20980.15790.04680.01440.24480.06170.2783-36.2359-14.4024-21.3947
40.96260.4662-0.38491.14430.08981.6201-0.11160.0504-0.1831-0.0010.13970.16080.1225-0.0894-0.02220.0904-0.01810.01990.08280.02510.1449-27.9594-26.6879-16.3553
50.51030.23370.45532.689-0.06281.369-0.0829-0.0374-0.00190.47890.0396-0.2444-0.0956-0.1740.1680.0924-0.00790.00840.08190.01140.1727-26.1034-23.3968-9.7775
61.33980.2916-0.34890.246-0.49070.81450.0649-0.3796-0.09550.05510.13720.0803-0.12280.025-0.1720.1549-0.01650.01870.28820.01780.2008-15.4002-22.222220.7969
71.44520.92990.69860.82650.53440.38340.2168-0.13670.8796-0.1029-0.36870.1436-0.3549-0.30390.1020.3174-0.02750.01960.3808-0.00030.463-25.8008-18.562315.2752
80.77360.39811.19961.0347-0.65813.79280.0725-0.5330.71330.21110.2120.4499-0.1472-0.7687-0.05810.24210.0050.13550.4265-0.09240.3589-19.4647-8.929722.4361
91.4202-0.3185-0.34332.36371.00541.3442-0.0053-0.1234-0.1109-0.09440.2553-0.2072-0.04940.2591-0.15050.1834-0.0305-0.0030.24860.02780.1661-15.6259-21.547415.2775
100.53780.01060.94141.2074-0.08031.38330.0513-1.22910.22470.139-0.05590.2787-0.1548-0.56980.27460.18360.00770.12160.4988-0.09590.2876-20.4158-15.286627.9753
111.4049-1.2062-0.46264.37530.442.5188-0.4076-0.2583-0.4075-0.06590.449-0.18370.05630.49920.14470.2371-0.02470.04760.1293-0.00480.2584-9.8166-25.7944-22.8464
120.5531-0.21810.32280.48390.28120.8650.03970.1695-0.07290.06560.0378-0.02580.14370.0333-0.01760.0775-0.03450.02240.1076-0.03310.1128-7.458-13.9752-17.6538
131.50650.52571.49831.3980.29432.9614-0.1737-0.09940.3924-0.17910.0230.2994-0.2564-0.19360.13840.1206-0.0071-0.00080.13620.00750.2-16.1076-8.8151-20.0451
141.35951.3816-0.79835.35862.47833.26670.07320.08751.04950.29760.18330.4490.05350.3629-0.13360.25810.010.03480.2057-0.11570.3647-18.0301-1.7131-13.793
151.9987-1.0171-1.31780.87011.77054.71640.14320.21160.0705-0.3511-0.2698-0.1607-0.78130.1513-0.02290.1839-0.04060.01110.1699-0.00640.1589-6.1778-9.0404-21.7745
160.83150.14990.3777-0.03990.08410.5556-0.05560.1131-0.11210.02410.1276-0.0819-0.09790.1235-0.03660.10720.0046-0.00180.0828-0.01540.1555-9.6969-12.0512-10.5902
171.87980.53160.98441.11690.54760.56450.2903-0.34510.39210.4161-0.08530.0799-0.42650.1737-0.10140.10990.00080.01420.1683-0.01950.1055-2.0832-19.793418.9305
181.6586-0.0706-0.35280.7460.84050.7993-0.002-0.2417-0.0935-0.02910.0131-0.0692-0.0183-0.0501-0.02070.0844-0.0029-0.02560.1210.03370.1332-6.1133-23.709714.5821
190.140.4582-0.44411.1739-0.83731.5878-0.1218-0.238-0.399-0.0418-0.1695-0.42160.12250.33740.24290.09810.01050.01430.21580.0860.18961.9925-28.115217.0447
200.738-0.48270.96121.9488-0.67671.2677-0.1907-1.06480.05970.40260.7869-0.61940.1887-1.387-0.46540.2870.0851-0.05860.56580.0530.1579-0.1477-27.998626.9785
210.0174-0.1004-0.09221.63671.0710.7121-0.09-0.01450.11440.81550.004-0.09040.11320.23550.02760.6832-0.1104-0.10520.39330.1370.2035-31.8409-34.6148-35.1025
220.58521.46481.18977.03661.93413.0070.39350.1241-0.32760.34030.01640.60910.38580.5091-0.32480.32340.0227-0.06970.20810.0190.2582-27.3205-26.9244-32.975
235.36884.01331.24094.50761.14270.322-0.47090.74450.2414-0.56390.54930.28360.11750.04990.00630.156-0.04510.01580.2054-0.03460.0756-21.75-19.3467-30.7627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:13)
2X-RAY DIFFRACTION2(chain A and resid 16:23)
3X-RAY DIFFRACTION3(chain A and resid 24:30C)
4X-RAY DIFFRACTION4(chain A and resid 30D:74)
5X-RAY DIFFRACTION5(chain A and resid 75:105)
6X-RAY DIFFRACTION6(chain A and resid 106:141)
7X-RAY DIFFRACTION7(chain A and resid 142:147)
8X-RAY DIFFRACTION8(chain A and resid 148:161)
9X-RAY DIFFRACTION9(chain A and resid 162:185)
10X-RAY DIFFRACTION10(chain A and resid 186:211)
11X-RAY DIFFRACTION11(chain B and resid 1:5)
12X-RAY DIFFRACTION12(chain B and resid 6:39)
13X-RAY DIFFRACTION13(chain B and resid 40:59)
14X-RAY DIFFRACTION14(chain B and resid 60:64)
15X-RAY DIFFRACTION15(chain B and resid 65:81)
16X-RAY DIFFRACTION16(chain B and resid 82:114)
17X-RAY DIFFRACTION17(chain B and resid 115:137)
18X-RAY DIFFRACTION18(chain B and resid 138:196)
19X-RAY DIFFRACTION19(chain B and resid 197:220)
20X-RAY DIFFRACTION20(chain B and resid 221:225)
21X-RAY DIFFRACTION21(chain P and resid 653:658)
22X-RAY DIFFRACTION22(chain P and resid 659:664)
23X-RAY DIFFRACTION23(chain P and resid 665:670)

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