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

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Basic information

Entry
Database: PDB / ID: 3mnv
TitleCrystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment
Components(ANTI-HIV-1 ANTIBODY 13H11 ...) x 2
KeywordsIMMUNE SYSTEM / HIV-1 / HIV / gp41 / MPER / 13H11 / 2F5 / Z13 / 4E10 / Fab antibody
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
: / : / 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 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
NITRATE ION / Ig-like domain-containing protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNicely, N.I. / Dennison, S.M. / Kelsoe, G. / Liao, H.-X. / Alam, S.M. / Haynes, B.F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Crystal structure of a non-neutralizing antibody to the HIV-1 gp41 membrane-proximal external region.
Authors: Nicely, N.I. / Dennison, S.M. / Spicer, L. / Scearce, R.M. / Kelsoe, G. / Ueda, Y. / Chen, H. / 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 1.2Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
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_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _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
A: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
B: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
C: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
D: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,40416
Polymers96,4824
Non-polymers92212
Water7,512417
1
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)48,84710
Polymers48,2412
Non-polymers6068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-25 kcal/mol
Surface area20570 Å2
MethodPISA
2
C: ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
D: ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5576
Polymers48,2412
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-24 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.378, 158.378, 92.975
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN


Mass: 24719.545 Da / Num. of mol.: 2 / Fragment: FUSION PROTEIN between mouse Fv and a 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
#2: Antibody ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN


Mass: 23521.475 Da / Num. of mol.: 2 / Fragment: FUSION PROTEIN between mouse Fv and a 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: Q6N089

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Non-polymers , 5 types, 429 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: Qiagen AmSO4 suite, reservoir: 2.2 M ammonium sulfate, 0.2 M lithium nitrate. Drop: 0.5 uL protein + 0.5 uL reservoir., 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: Aug 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.278 Å / Num. all: 51941 / Num. obs: 51525 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.4

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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: 1MHH, 1TJG

1mhh

1tjg


Resolution: 2.4→45.278 Å / SU ML: 0.35 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1983 3.87 %
Rwork0.1808 --
obs0.1826 51189 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.154 Å2 / ksol: 0.406 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→45.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6595 0 51 417 7063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086839
X-RAY DIFFRACTIONf_angle_d1.0759288
X-RAY DIFFRACTIONf_dihedral_angle_d15.4072411
X-RAY DIFFRACTIONf_chiral_restr0.0721039
X-RAY DIFFRACTIONf_plane_restr0.0051176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46020.22691360.19373439X-RAY DIFFRACTION98
2.4602-2.52670.26851410.19083514X-RAY DIFFRACTION98
2.5267-2.6010.27161430.20843505X-RAY DIFFRACTION99
2.601-2.6850.25411410.19823518X-RAY DIFFRACTION99
2.685-2.78090.29471410.19573511X-RAY DIFFRACTION99
2.7809-2.89230.27631420.19513498X-RAY DIFFRACTION99
2.8923-3.02390.24181430.18873519X-RAY DIFFRACTION99
3.0239-3.18330.25171440.18143536X-RAY DIFFRACTION99
3.1833-3.38260.2171410.1733506X-RAY DIFFRACTION99
3.3826-3.64370.19971420.15743527X-RAY DIFFRACTION99
3.6437-4.01020.21341410.153530X-RAY DIFFRACTION99
4.0102-4.590.1731430.12933532X-RAY DIFFRACTION99
4.59-5.7810.17851410.1383528X-RAY DIFFRACTION98
5.781-45.28650.22281440.20463543X-RAY DIFFRACTION97
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.8388-0.5141-0.92921.31621.09581.3235-0.27340.72470.13550.1322-0.30450.29730.5908-0.15560.10880.5013-0.08770.0310.33660.14150.2805106.3835-27.192141.6919
20.4253-0.45520.17711.25360.37560.2007-0.2449-0.01250.21180.47690.0622-0.1861-0.5505-0.14220.12450.5263-0.03780.00070.17740.02170.2618
34.5281-3.83231.84363.4291-2.35033.7795-0.16770.00360.77170.231-0.0425-0.2861-1.21490.07070.24080.5570.0719-0.01170.29140.00150.3298
41.5438-1.56241.2943.7647-0.7962.20850.594-0.55120.5076-0.44850.03741.955-0.1867-1.1553-0.08010.39760.19430.03570.713-0.05330.7935
53.01510.10041.48482.39090.35282.8380.2451-0.2646-0.23820.4918-0.04260.03550.5194-0.3011-0.1510.3944-0.00520.02980.16980.03720.1201
61.721-0.06671.90460.62431.14791.79460.05840.02490.0790.13280.0043-0.0883-0.150.0435-0.01440.4416-0.00790.02170.17450.00410.1961
75.4355-1.3042-1.03061.6768-0.35942.3518-0.08560.20310.62910.1927-0.0379-0.9609-0.45710.2615-0.19680.373-0.12070.06110.18320.0590.2749
84.32990.54312.25410.9761.36633.2241-0.4370.71811.6696-1.7875-0.1225-0.2143-1.4285-0.03560.01660.7923-0.25970.17950.51870.28650.9066
91.8797-1.4289-0.88781.4787-0.03282.91270.0731-0.02740.1556-0.1315-0.2033-0.2448-0.2706-0.16320.01920.4207-0.08230.01990.24540.04930.2808
103.8499-1.2323-2.14160.6064-0.44813.85610.2268-0.18441.3319-0.40960.1903-0.821-0.84540.6401-0.31850.4843-0.28290.15150.50070.05650.67
110.9182-0.79671.2394.1965-2.85263.30490.49550.0188-0.4524-0.48380.31940.5827-0.0137-0.1983-0.5390.444600.11850.35030.08120.5697
121.4125-0.45051.431.5678-0.38551.53360.1889-0.0963-0.3727-0.5073-0.02250.13270.3114-0.0771-0.16580.39870.0038-0.06240.17310.05250.2321
135.9241-0.82420.05242.1641-0.15840.2821-0.0145-0.16390.7467-0.32470.1560.0004-0.09230.10740.01950.3464-0.00530.01740.1709-0.00440.1595
142.3955-0.9192-1.11150.8565-0.34981.93610.37510.62580.9359-0.41980.0710.4679-0.1671-0.5628-0.25350.38970.0155-0.02850.28080.10660.169
152.3469-0.5448-1.18642.0904-0.42961.45560.69860.52730.13880.0944-0.0397-0.0591-0.1499-0.6581-0.4790.45030.0562-0.08180.27960.02430.1115
166.60753.70170.94275.91931.140.28030.37350.99580.0499-0.77-0.09450.44720.2495-0.2421-0.21710.4131-0.0052-0.12350.25250.01920.2194
171.8821-1.3841-1.45914.2762-0.43445.08480.59640.34190.6728-0.2491-0.7170.29340.0524-0.3855-0.15110.4616-0.01510.07250.18590.07980.1973
182.0763-0.2452-1.33590.8463-0.20451.0683-0.0256-0.20870.102-0.0167-0.04390.00970.08320.16540.02670.37090.00750.01520.1988-0.03760.1522
191.6563-0.4937-0.60181.773-1.03742.17980.12430.10740.071-0.2763-0.1016-0.1117-0.094-0.035-0.06430.24930.00180.09440.13570.00750.1591
206.02342.8666-0.51171.58370.26633.3619-0.2442-0.3126-0.9149-0.94120.1275-0.1345-0.00810.43660.13040.44670.11830.12210.2269-0.01050.4131
213.685-0.5096-5.03946.99353.54188.06120.4430.67050.34971.23510.3285-0.6621.3485-0.5553-0.16460.524-0.319-0.10260.63770.4020.6514
221.5789-1.83551.02592.6742-0.31991.60160.69390.1495-1.0733-0.56310.08730.93710.6492-0.0602-0.48370.5634-0.0431-0.20350.21-0.07030.4691
231.6527-0.40020.7640.204-0.1210.61740.14210.2856-1.2828-0.08190.1990.90650.61610.0153-0.36240.7082-0.1787-0.25510.27160.09160.8666
249.33393.20975.32533.77021.15113.20840.1606-1.03850.1673-0.8183-0.07091.61160.1309-0.24160.00670.4883-0.125-0.26770.47870.06620.8014
252.1559-1.01890.79253.65810.20451.45580.28950.0326-0.3478-0.3886-0.02690.23410.33520.0707-0.27050.3743-0.0432-0.09450.17380.00610.3025
263.09010.50091.47360.506-0.31391.2524-0.1227-0.8851-0.8527-0.36230.43020.76550.5111-0.191-0.33450.3012-0.0966-0.09510.23350.16020.5154
270.8299-1.30950.16742.8640.27830.936-0.239-0.0192-0.24590.16820.2104-0.14480.05850.16750.02070.32610.0210.06820.1831-0.03020.2054
281.892-2.7414-1.12616.22033.92773.4533-0.6708-0.126-0.67531.02320.91161.22231.1339-0.13920.11010.6559-0.10990.19490.36320.0510.5804
290.41380.598-0.16370.7788-0.61965.9408-0.2407-0.1388-0.3046-0.0689-0.1480.16781.1881-0.19670.28740.54810.17990.13510.1850.04380.2792
303.4136-0.5957-0.40090.33710.37386.745-0.2586-0.4246-0.55590.69050.19570.18841.95890.43190.12220.65730.22020.12910.22740.02610.2651
311.58710.2318-3.22890.5594-0.90626.84780.09730.5668-1.43910.6137-0.3159-0.7075-1.10410.5599-0.02430.462-0.09060.10080.3702-0.11520.2721
320.5423-0.69881.27080.8179-1.84385.5202-0.0988-0.1249-0.05730.01880.27440.2773-0.5069-0.1098-0.22830.4507-0.01170.1180.27850.06640.3612
332.8693-0.97682.0410.3438-0.31827.00050.78990.1931-0.3613-0.2144-0.41290.34880.39050.0649-0.41130.3023-0.05960.00250.32220.11870.3516
342.0804-2.09061.1772.0203-1.06486.2739-0.1152-0.27630.11690.4790.60580.2781-0.9273-0.8032-0.54920.32470.12540.19080.37220.17310.3365
350.64740.1635-0.3381.36370.37193.48860.0125-0.2737-0.17860.4318-0.14980.17780.5589-1.9502-0.21460.49490.05030.16620.60940.23610.4692
361.21790.14660.96761.5463-0.94762.67860.0925-0.136-0.0514-0.13960.29350.2074-0.39710.1463-0.27340.1949-0.02460.06380.14520.03970.1582
373.6974-1.281-0.12885.911.73360.9538-0.0624-0.1703-0.55020.55490.16440.30010.0960.2827-0.14150.23430.0427-0.08580.141-0.01330.1186
381.1012-0.75950.12911.39930.16781.07830.07230.1565-0.0852-0.01120.04610.00370.21650.05-0.06130.2608-0.02070.02090.1855-0.0140.1705
391.78180.3715-2.01121.51650.05493.87510.3352-0.40980.3520.09620.0396-0.2034-0.420.4863-0.37830.23950.0290.00650.1778-0.03950.1374
401.5261-1.7223-0.57427.8975-1.5492.15090.37190.15210.2991-0.2101-1.1015-0.72780.51231.12570.49550.3690.1338-0.11010.4760.04780.2681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -2:3)A-2 - 3
2X-RAY DIFFRACTION2(chain A and resid 4:21)A4 - 21
3X-RAY DIFFRACTION3(chain A and resid 22:29)A22 - 29
4X-RAY DIFFRACTION4(chain A and resid 30:30F)A30
5X-RAY DIFFRACTION5(chain A and resid 31:69)A31 - 69
6X-RAY DIFFRACTION6(chain A and resid 70:109)A70 - 109
7X-RAY DIFFRACTION7(chain A and resid 110:146)A110 - 146
8X-RAY DIFFRACTION8(chain A and resid 147:158)A147 - 158
9X-RAY DIFFRACTION9(chain A and resid 159:184)A159 - 184
10X-RAY DIFFRACTION10(chain A and resid 185:213)A185 - 213
11X-RAY DIFFRACTION11(chain B and resid 0:4)B0 - 4
12X-RAY DIFFRACTION12(chain B and resid 5:30)B5 - 30
13X-RAY DIFFRACTION13(chain B and resid 31:49)B31 - 49
14X-RAY DIFFRACTION14(chain B and resid 50:64)B50 - 64
15X-RAY DIFFRACTION15(chain B and resid 65:72)B65 - 72
16X-RAY DIFFRACTION16(chain B and resid 73:82A)B73 - 82
17X-RAY DIFFRACTION17(chain B and resid 82B:85)B82
18X-RAY DIFFRACTION18(chain B and resid 86:114)B86 - 114
19X-RAY DIFFRACTION19(chain B and resid 115:215)B115 - 215
20X-RAY DIFFRACTION20(chain B and resid 216:226)B216 - 226
21X-RAY DIFFRACTION21(chain C and resid -1:3)C-1 - 3
22X-RAY DIFFRACTION22(chain C and resid 4:21)C4 - 21
23X-RAY DIFFRACTION23(chain C and resid 22:30)C22 - 30
24X-RAY DIFFRACTION24(chain C and resid 30A:30E)C30
25X-RAY DIFFRACTION25(chain C and resid 30F:93)C30
26X-RAY DIFFRACTION26(chain C and resid 94:105)C94 - 105
27X-RAY DIFFRACTION27(chain C and resid 106:141)C106 - 141
28X-RAY DIFFRACTION28(chain C and resid 142:147)C142 - 147
29X-RAY DIFFRACTION29(chain C and resid 148:195)C148 - 195
30X-RAY DIFFRACTION30(chain C and resid 196:212)C196 - 212
31X-RAY DIFFRACTION31(chain D and resid 1:5)D1 - 5
32X-RAY DIFFRACTION32(chain D and resid 6:40)D6 - 40
33X-RAY DIFFRACTION33(chain D and resid 41:53)D41 - 53
34X-RAY DIFFRACTION34(chain D and resid 54:80)D54 - 80
35X-RAY DIFFRACTION35(chain D and resid 81:85)D81 - 85
36X-RAY DIFFRACTION36(chain D and resid 86:116)D86 - 116
37X-RAY DIFFRACTION37(chain D and resid 117:127)D117 - 127
38X-RAY DIFFRACTION38(chain D and resid 136:194)D136 - 194
39X-RAY DIFFRACTION39(chain D and resid 195:221)D195 - 221
40X-RAY DIFFRACTION40(chain D and resid 222:226)D222 - 226

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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