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- PDB-6p60: Vaccine-elicited NHP FP-targeting neutralizing antibody A12V163-a... -

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Basic information

Entry
Database: PDB / ID: 6p60
TitleVaccine-elicited NHP FP-targeting neutralizing antibody A12V163-a.02 in complex with HIV fusion peptide (residue 512-519)
Components
  • Antibody A12V163-a.02 heavy chain
  • Antibody A12V163-a.02 light chain
  • HIV fusion peptide residue 512-519
KeywordsIMMUNE SYSTEM / HIV / neutralizing / NHP / FP / Fusion Peptide / vaccine
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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesPlatyrrhini (New World monkeys)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.498 Å
AuthorsXu, K. / Liu, K. / Kwong, P.D.
CitationJournal: To Be Published
Title: Vaccine-elicited NHP FP-targeting neutralizing antibody A12V163-a.02 in complex with HIV fusion peptide (residue 512-519)
Authors: Xu, K. / Liu, K. / Kwong, P.D.
History
DepositionMay 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody A12V163-a.02 heavy chain
B: Antibody A12V163-a.02 light chain
E: HIV fusion peptide residue 512-519
C: Antibody A12V163-a.02 heavy chain
D: Antibody A12V163-a.02 light chain
F: HIV fusion peptide residue 512-519
G: Antibody A12V163-a.02 heavy chain
H: Antibody A12V163-a.02 light chain
I: HIV fusion peptide residue 512-519
J: Antibody A12V163-a.02 heavy chain
K: Antibody A12V163-a.02 light chain
L: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)189,20712
Polymers189,20712
Non-polymers00
Water16,754930
1
A: Antibody A12V163-a.02 heavy chain
B: Antibody A12V163-a.02 light chain
E: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,3023
Polymers47,3023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-33 kcal/mol
Surface area19500 Å2
MethodPISA
2
C: Antibody A12V163-a.02 heavy chain
D: Antibody A12V163-a.02 light chain
F: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,3023
Polymers47,3023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-34 kcal/mol
Surface area19490 Å2
MethodPISA
3
G: Antibody A12V163-a.02 heavy chain
H: Antibody A12V163-a.02 light chain
I: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,3023
Polymers47,3023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-30 kcal/mol
Surface area19580 Å2
MethodPISA
4
J: Antibody A12V163-a.02 heavy chain
K: Antibody A12V163-a.02 light chain
L: HIV fusion peptide residue 512-519


Theoretical massNumber of molelcules
Total (without water)47,3023
Polymers47,3023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-30 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.784, 72.199, 185.526
Angle α, β, γ (deg.)90.000, 96.630, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 135 or resid 142 through 222))
21(chain C and (resid 2 through 135 or resid 142 through 222))
31chain G
41chain J
12chain B
22chain D
32(chain H and resid 2 through 212)
42(chain K and resid 2 through 212)
13chain E
23chain F
33chain I
43chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALPROPRO(chain A and (resid 2 through 135 or resid 142 through 222))AA2 - 1352 - 135
121GLUGLUILEILE(chain A and (resid 2 through 135 or resid 142 through 222))AA142 - 222142 - 222
211VALVALPROPRO(chain C and (resid 2 through 135 or resid 142 through 222))CD2 - 1352 - 135
221GLUGLUILEILE(chain C and (resid 2 through 135 or resid 142 through 222))CD142 - 222142 - 222
311VALVALILEILEchain GGG2 - 2222 - 222
411VALVALILEILEchain JJJ2 - 2222 - 222
112PHEPHEPROPROchain BBB2 - 2122 - 212
212PHEPHEPROPROchain DDE2 - 2122 - 212
312PHEPHEPROPRO(chain H and resid 2 through 212)HH2 - 2122 - 212
412PHEPHEPROPRO(chain K and resid 2 through 212)KK2 - 2122 - 212
113ALAALAPHEPHEchain EEC512 - 5191 - 8
213ALAALAPHEPHEchain FFF512 - 5191 - 8
313ALAALAPHEPHEchain III512 - 5191 - 8
413ALAALAPHEPHEchain LLL512 - 5191 - 8

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
Antibody A12V163-a.02 heavy chain


Mass: 24081.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Platyrrhini (New World monkeys) / Production host: Homo sapiens (human)
#2: Antibody
Antibody A12V163-a.02 light chain


Mass: 22487.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Platyrrhini (New World monkeys) / Production host: Homo sapiens (human)
#3: Protein/peptide
HIV fusion peptide residue 512-519


Mass: 732.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 930 / 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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.15M AMSO4, 0.1 M acetate pH 4.5 25.5% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 69828 / % possible obs: 98.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.058 / Rrim(I) all: 0.111 / Χ2: 1.543 / Net I/σ(I): 7.1 / Num. measured all: 249782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.30.48633330.9120.3010.5740.83995.9
2.54-2.593.40.41933860.9220.2590.4940.993.8
2.59-2.643.40.39233880.9420.2420.4620.91297.4
2.64-2.693.40.36733670.9370.2270.4321.06595.7
2.69-2.753.40.31334290.9620.1930.3691.0498.1
2.75-2.823.50.28834410.9640.1770.3381.12297.6
2.82-2.893.50.23734910.9690.1460.2791.23297.8
2.89-2.963.50.21134990.9740.1290.2481.29699.7
2.96-3.053.60.19334660.9810.1170.2261.40198.5
3.05-3.153.60.1735040.9820.1030.1991.46998.7
3.15-3.263.70.14735420.9850.090.1731.58899.7
3.26-3.393.70.12934890.9880.0780.1511.67699.2
3.39-3.553.70.12335200.9860.0750.1442.00899.1
3.55-3.733.70.10535090.990.0640.1232.18699.3
3.73-3.973.70.09635330.9910.0590.1132.31699.4
3.97-4.273.70.07935530.9940.0480.0932.36399.4
4.27-4.73.70.07135270.9940.0430.0832.41499.6
4.7-5.383.70.06435610.9940.0390.0752.09699.6
5.38-6.783.70.05435900.9960.0330.0631.37999.6
6.78-503.60.03337000.9980.020.0390.98399.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.498→41.746 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 3374 4.85 %
Rwork0.1965 66211 -
obs0.1971 69585 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.32 Å2 / Biso mean: 44.1607 Å2 / Biso min: 19.71 Å2
Refinement stepCycle: final / Resolution: 2.498→41.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13078 0 0 930 14008
Biso mean---49.86 -
Num. residues----1750
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3917X-RAY DIFFRACTION11.363TORSIONAL
12C3917X-RAY DIFFRACTION11.363TORSIONAL
13G3917X-RAY DIFFRACTION11.363TORSIONAL
14J3917X-RAY DIFFRACTION11.363TORSIONAL
21B3825X-RAY DIFFRACTION11.363TORSIONAL
22D3825X-RAY DIFFRACTION11.363TORSIONAL
23H3825X-RAY DIFFRACTION11.363TORSIONAL
24K3825X-RAY DIFFRACTION11.363TORSIONAL
31E108X-RAY DIFFRACTION11.363TORSIONAL
32F108X-RAY DIFFRACTION11.363TORSIONAL
33I108X-RAY DIFFRACTION11.363TORSIONAL
34L108X-RAY DIFFRACTION11.363TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4983-2.5340.34151060.30572375248185
2.534-2.57180.33771320.28262636276893
2.5718-2.6120.32831360.28012651278796
2.612-2.65480.31931260.28572747287396
2.6548-2.70060.31651500.27612658280896
2.7006-2.74970.31991460.25652723286998
2.7497-2.80250.27691450.24982758290397
2.8025-2.85970.22081210.23932799292099
2.8597-2.92190.27721440.22892719286398
2.9219-2.98980.25821580.23232811296999
2.9898-3.06460.24771430.21772712285599
3.0646-3.14740.24641430.2092797294098
3.1474-3.240.20461500.203427892939100
3.24-3.34450.24881560.20292759291599
3.3445-3.4640.20741510.19432778292999
3.464-3.60260.20311340.18952817295199
3.6026-3.76650.17771080.17962843295199
3.7665-3.96490.19061300.17222808293899
3.9649-4.21310.16231760.157227982974100
4.2131-4.53810.14461340.15262834296899
4.5381-4.99410.16261510.149228152966100
4.9941-5.71520.18091350.176328542989100
5.7152-7.19450.22131550.202628723027100
7.1945-41.75230.17341440.20112858300297

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