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

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Basic information

Entry
Database: PDB / ID: 3mnz
TitleCrystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41 MPER-derived peptide bearing Ala substitutions in a helical conformation
Components
  • ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
  • ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
  • gp41 MPER-derived peptide
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 / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / metal ion binding / 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 ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / 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: 1.8 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 1.2Oct 5, 2011Group: Derived calculations
Revision 1.3Jun 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.ncbi_taxonomy_id ..._entity.pdbx_fragment / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _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 1.4Sep 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_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 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
P: gp41 MPER-derived peptide
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)50,5934
Polymers50,5703
Non-polymers231
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-30 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.890, 121.692, 58.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11P-394-

HOH

21P-447-

HOH

31P-550-

HOH

41B-420-

HOH

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Components

#1: Protein/peptide gp41 MPER-derived peptide


Mass: 2328.601 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.2
Details: Reservoir: Qiagen Classics II, condition with 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: Oct 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. all: 44756 / Num. obs: 44756 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.8

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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: 1.8→45 Å / SU ML: 0.23 / σ(F): 0.11 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 1984 4.47 %
Rwork0.1787 --
obs0.1803 44353 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.676 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.8369 Å2-0 Å20 Å2
2---5.0244 Å2-0 Å2
3---0.1875 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 1 567 3971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083516
X-RAY DIFFRACTIONf_angle_d1.1034787
X-RAY DIFFRACTIONf_dihedral_angle_d15.5591245
X-RAY DIFFRACTIONf_chiral_restr0.075540
X-RAY DIFFRACTIONf_plane_restr0.011608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.25281390.19292958X-RAY DIFFRACTION98
1.845-1.89490.26091380.18782948X-RAY DIFFRACTION99
1.8949-1.95070.24841380.19212959X-RAY DIFFRACTION98
1.9507-2.01360.23521420.18083019X-RAY DIFFRACTION99
2.0136-2.08560.23861380.18532951X-RAY DIFFRACTION98
2.0856-2.16910.26311410.17262995X-RAY DIFFRACTION99
2.1691-2.26780.2191400.18562991X-RAY DIFFRACTION99
2.2678-2.38740.22971420.18373036X-RAY DIFFRACTION99
2.3874-2.53690.1961410.18183019X-RAY DIFFRACTION99
2.5369-2.73280.23041420.18053012X-RAY DIFFRACTION99
2.7328-3.00780.2331440.18523055X-RAY DIFFRACTION100
3.0078-3.44290.19381430.16923071X-RAY DIFFRACTION100
3.4429-4.33710.17171450.14333104X-RAY DIFFRACTION100
4.3371-45.02410.17691510.15983251X-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)
10.03470.15760.17393.94710.37830.6639-0.03360.01580.171-0.21550.0437-0.8393-0.16920.2269-0.03530.1391-0.01630.01690.2774-0.00020.257325.23999.7854-13.3106
20.1026-0.487-0.30344.42760.81370.99540.06340.02430.0278-0.9849-0.0633-0.0971-0.2910.0792-0.00040.2212-0.0004-0.01680.14570.01840.121619.857110.3428-19.2572
32.8649-2.1519-1.42695.25971.34191.3317-0.19610.3272-0.2883-0.9151-0.1380.1309-0.4987-0.08530.22160.37860.0641-0.0760.2373-0.09490.252213.7997-6.9533-27.314
40.0004-0.0413-0.07452.87240.37990.549-0.0292-0.0243-0.0435-0.3908-0.06830.3344-0.1247-0.00490.07580.16770.0224-0.08140.125-0.01030.149212.6518.4975-13.9862
50.1315-0.4357-0.24381.35150.65410.8641-0.1292-0.09290.05680.18990.2336-0.21290.11240.3334-0.0730.14650.0606-0.01930.22910.00730.165921.18478.2835-9.4553
60.71580.56120.311.74630.59330.2782-0.0819-0.10820.07820.16190.00550.0282-0.4983-0.01830.04230.1349-0.01550.0270.1353-0.00870.115828.219129.456215.056
71.15110.0081.14660.498-0.08241.13550.1241-0.0367-0.1407-0.06160.06850.0093-0.0196-0.0634-0.12860.1086-0.0070.00580.1012-0.01330.087533.409125.141312.8445
81.2045-0.6120.31540.9602-0.22820.41480.2050.0607-0.3548-0.25860.0068-0.06630.07790.0576-0.13950.16760.0126-0.01720.1476-0.04230.176432.741219.1910.4454
91.3238-0.05621.37180.6028-0.1411.33660.24580.002-0.1504-0.0678-0.02970.05650.05060.0167-0.14190.1075-0.0052-0.00340.16310.01390.118528.760423.33713.7605
101.21160.51361.08530.74870.4622.2204-0.13850.1872-0.0693-0.06110.1483-0.1123-0.54250.2807-0.00660.1763-0.06490.04610.1824-0.0110.111538.333131.441614.0196
110.0648-0.17120.33420.9988-1.06053.52080.0965-0.1156-0.057-0.05460.0260.4307-0.1523-0.9076-0.05220.15550.05330.00180.324-0.03330.29254.2553-4.0195-0.9371
120.16980.13750.59811.79661.07962.131-0.1115-0.0781-0.04160.1036-0.05050.31420.0047-0.22480.14430.1024-0.00360.01320.12590.01370.178414.1781-7.92823.6129
134.28282.7854.03991.97813.29846.7585-0.47230.16910.416-0.5793-0.00040.0715-1.37920.56590.42840.3635-0.0974-0.02530.13040.01120.176223.60190.0907-1.9109
144.0669-2.15470.33011.2298-0.60442.53380.14530.0071-0.4308-0.1849-0.0410.30250.4470.1309-0.12720.17650.0265-0.01160.1480.00170.173619.2713-15.6967-5.6044
152.1088-0.47790.751.29090.41340.8203-0.0290.0031-0.2920.33830.0820.15780.2633-0.0045-0.0390.16450.00890.0090.1360.03860.204419.2948-12.71994.0916
160.1795-0.1683-0.18270.5156-0.24630.7077-0.0702-0.0831-0.03910.07080.0480.0703-0.2012-0.1416-0.01310.13520.0124-0.01940.1230.00560.151618.4751-1.27353.8415
171.0375-0.19260.0590.4411-0.00920.70090.0846-0.10690.11770.03620.01850.0677-0.0924-0.0363-0.090.11310.010.03090.12310.00520.151120.870619.963319.8469
182.12-0.1587-2.31290.06250.4544.06990.464-0.16360.78310.08260.14150.293-0.45620.1705-0.54210.4912-0.01550.07810.2342-0.06870.450617.400240.013124.5837
191.556-0.41940.63220.1341-0.12210.34760.1267-0.3013-0.15520.27810.0170.1476-0.1026-0.32790.12610.13570.00130.08330.26780.040.213714.069518.086126.6858
204.8023.99730.40023.64851.42363.7255-0.0397-0.3573-0.0869-0.58070.1879-0.3202-0.50830.1016-0.13140.21220.0110.03750.2031-0.10410.206820.569630.099729.5784
213.7630.5214-3.73671.1341-0.63866.5498-0.14160.6663-0.33890.0554-0.01420.0405-0.2668-0.85980.12130.29280.0438-0.06270.3991-0.12460.33180.9194-5.3512-24.4814
224.7199-1.38154.52851.0294-3.15089.73690.4176-0.2179-0.4247-0.3587-0.11250.6511.0715-0.0729-0.3450.1987-0.0184-0.07550.0916-0.03260.2657.9601-9.3395-17.2953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 0:13)
2X-RAY DIFFRACTION2(chain A and resid 14:30A)
3X-RAY DIFFRACTION3(chain A and resid 30B:30F)
4X-RAY DIFFRACTION4(chain A and resid 31:92)
5X-RAY DIFFRACTION5(chain A and resid 93:107)
6X-RAY DIFFRACTION6(chain A and resid 108:124)
7X-RAY DIFFRACTION7(chain A and resid 125:153)
8X-RAY DIFFRACTION8(chain A and resid 154:165)
9X-RAY DIFFRACTION9(chain A and resid 166:187)
10X-RAY DIFFRACTION10(chain A and resid 188:213)
11X-RAY DIFFRACTION11(chain B and resid 1:6)
12X-RAY DIFFRACTION12(chain B and resid 7:39)
13X-RAY DIFFRACTION13(chain B and resid 40:48)
14X-RAY DIFFRACTION14(chain B and resid 49:61)
15X-RAY DIFFRACTION15(chain B and resid 62:82C)
16X-RAY DIFFRACTION16(chain B and resid 83:114)
17X-RAY DIFFRACTION17(chain B and resid 115:194)
18X-RAY DIFFRACTION18(chain B and resid 195:203)
19X-RAY DIFFRACTION19(chain B and resid 205:220)
20X-RAY DIFFRACTION20(chain B and resid 221:225)
21X-RAY DIFFRACTION21(chain P and resid 656:662)
22X-RAY DIFFRACTION22(chain P and resid 663:670)

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